Build issue when using package restore in Team Foundation Service - tfs

Question

I'm trying Microsoft Team Foundation Service ( the Cloud TFS ) and using automated hosted build and package restore.
It always fails, but according to log it seems that the package restore works fine but it's a problem when locating the binaries we got through the package restore, it's like it doesn't look into the right folder.
LOG:
Build started 4/9/2013 10:24:37 AM.
Project "C:\a\src\ValuePlan.Client.sln" on node 1 (default targets).
ValidateSolutionConfiguration:
Building solution configuration "Release|x86".
Project "C:\a\src\ValuePlan.Client.sln" (1) is building "C:\a\src\VP\VP.csproj" (2) on node 1 (default targets).
RestorePackages:
"C:\a\src\.nuget\nuget.exe" install "C:\a\src\VP\packages.config" -source "" -o "C:\a\src\packages"
Successfully installed 'Autofac 2.6.3.862'.
Successfully installed 'Caliburn.Micro 1.3.1'.
PrepareForBuild:
Creating directory "obj\x86\Release\".
Project "C:\a\src\VP\VP.csproj" (2) is building "C:\a\src\VpUserControls\VpUserControls.csproj" (3) on node 1 (default targets).
RestorePackages:
"C:\a\src\.nuget\nuget.exe" install "C:\a\src\VpUserControls\packages.config" -source "" -o "C:\a\src\packages"
All packages listed in packages.config are already installed.
PrepareForBuild:
Creating directory "obj\Release\".
ResolveAssemblyReferences:
A TargetFramework profile exclusion list will be generated.
Primary reference "Caliburn.Micro".
C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Microsoft.Common.targets(1578,5): warning MSB3245: Could not resolve this reference. Could not locate the assembly "Caliburn.Micro". Check to make sure the assembly exists on disk. If this reference is required by your code, you may get compilation errors. [C:\a\src\VpUserControls\VpUserControls.csproj]
For SearchPath "C:\a\src\VpUserControls\FakesAssemblies".
Considered "C:\a\src\VpUserControls\FakesAssemblies\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\a\src\VpUserControls\FakesAssemblies\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\a\src\VpUserControls\FakesAssemblies\Caliburn.Micro.exe", but it didn't exist.
For SearchPath "{HintPathFromItem}".
Considered "..\..\CL_WIN\packages\Caliburn.Micro.1.3.1\lib\net40\Caliburn.Micro.dll", but it didn't exist.
For SearchPath "{TargetFrameworkDirectory}".
Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\Caliburn.Micro.exe", but it didn't exist.
For SearchPath "{Registry:Software\Microsoft\.NETFramework,v4.0,AssemblyFoldersEx}".
Considered AssemblyFoldersEx locations.
For SearchPath "{AssemblyFolders}".
Considered "C:\Program Files\Microsoft.NET\ADOMD.NET\100\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft.NET\ADOMD.NET\100\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft.NET\ADOMD.NET\100\Caliburn.Micro.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\110\SDK\Assemblies\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\110\SDK\Assemblies\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\110\SDK\Assemblies\Caliburn.Micro.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\Tasks\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\Tasks\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\Tasks\Caliburn.Micro.exe", but it didn't exist.
Considered "C:\Program Files\IIS\Microsoft Web Deploy V3\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\IIS\Microsoft Web Deploy V3\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\IIS\Microsoft Web Deploy V3\Caliburn.Micro.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\PipelineComponents\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\PipelineComponents\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\PipelineComponents\Caliburn.Micro.exe", but it didn't exist.
Considered "C:\Program Files\Reference Assemblies\Microsoft\Framework\v3.5\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\Reference Assemblies\Microsoft\Framework\v3.5\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\Reference Assemblies\Microsoft\Framework\v3.5\Caliburn.Micro.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\ForEachEnumerators\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\ForEachEnumerators\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\ForEachEnumerators\Caliburn.Micro.exe", but it didn't exist.
For SearchPath "{GAC}".
Considered "Caliburn.Micro", which was not found in the GAC.
For SearchPath "{RawFileName}".
Considered treating "Caliburn.Micro" as a file name, but it didn't exist.
For SearchPath "C:\a\bin\".
Considered "C:\a\bin\Caliburn.Micro.winmd", but it didn't exist.
Considered "C:\a\bin\Caliburn.Micro.dll", but it didn't exist.
Considered "C:\a\bin\Caliburn.Micro.exe", but it didn't exist.
Primary reference "System.Windows.Interactivity".
C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Microsoft.Common.targets(1578,5): warning MSB3245: Could not resolve this reference. Could not locate the assembly "System.Windows.Interactivity". Check to make sure the assembly exists on disk. If this reference is required by your code, you may get compilation errors. [C:\a\src\VpUserControls\VpUserControls.csproj]
For SearchPath "C:\a\src\VpUserControls\FakesAssemblies".
Considered "C:\a\src\VpUserControls\FakesAssemblies\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\a\src\VpUserControls\FakesAssemblies\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\a\src\VpUserControls\FakesAssemblies\System.Windows.Interactivity.exe", but it didn't exist.
For SearchPath "{HintPathFromItem}".
Considered "..\..\CL_WIN\packages\Caliburn.Micro.1.3.1\lib\net40\System.Windows.Interactivity.dll", but it didn't exist.
For SearchPath "{TargetFrameworkDirectory}".
Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\System.Windows.Interactivity.exe", but it didn't exist.
For SearchPath "{Registry:Software\Microsoft\.NETFramework,v4.0,AssemblyFoldersEx}".
Considered AssemblyFoldersEx locations.
For SearchPath "{AssemblyFolders}".
Considered "C:\Program Files\Microsoft.NET\ADOMD.NET\100\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft.NET\ADOMD.NET\100\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft.NET\ADOMD.NET\100\System.Windows.Interactivity.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\110\SDK\Assemblies\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\110\SDK\Assemblies\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\110\SDK\Assemblies\System.Windows.Interactivity.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\Tasks\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\Tasks\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\Tasks\System.Windows.Interactivity.exe", but it didn't exist.
Considered "C:\Program Files\IIS\Microsoft Web Deploy V3\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\IIS\Microsoft Web Deploy V3\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\IIS\Microsoft Web Deploy V3\System.Windows.Interactivity.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\PipelineComponents\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\PipelineComponents\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\PipelineComponents\System.Windows.Interactivity.exe", but it didn't exist.
Considered "C:\Program Files\Reference Assemblies\Microsoft\Framework\v3.5\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\Reference Assemblies\Microsoft\Framework\v3.5\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\Reference Assemblies\Microsoft\Framework\v3.5\System.Windows.Interactivity.exe", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\ForEachEnumerators\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\ForEachEnumerators\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\Program Files\Microsoft SQL Server\100\DTS\ForEachEnumerators\System.Windows.Interactivity.exe", but it didn't exist.
For SearchPath "{GAC}".
Considered "System.Windows.Interactivity", which was not found in the GAC.
For SearchPath "{RawFileName}".
Considered treating "System.Windows.Interactivity" as a file name, but it didn't exist.
For SearchPath "C:\a\bin\".
Considered "C:\a\bin\System.Windows.Interactivity.winmd", but it didn't exist.
Considered "C:\a\bin\System.Windows.Interactivity.dll", but it didn't exist.
Considered "C:\a\bin\System.Windows.Interactivity.exe", but it didn't exist.
AssemblyFoldersEx location: "{Registry:Software\Microsoft\.NETFramework,v4.0,AssemblyFoldersEx}"
C:\Program Files (x86)\Microsoft XNA\XNA Game Studio\v4.0\References\Windows\x86\
C:\Program Files\Reference Assemblies\Microsoft\Workflow Manager\1.0\
C:\Program Files\Microsoft SDKs\Windows Azure\.NET SDK\2012-10\ref\Caching\
C:\Program Files\Windows Azure SDK\v1.6\ServiceBus\ref\
C:\Program Files\Windows Azure SDK\v1.6\Cache\ref\
C:\Program Files (x86)\Microsoft WCF Data Services\5.0\bin\.NETFramework\
C:\Program Files (x86)\Common Files\microsoft shared\VSTT\10.0\UITestExtensionPackages
C:\Program Files\Reference Assemblies\Microsoft\VSTO40\v4.0.Framework\
C:\Program Files\Reference Assemblies\Microsoft\VSTA30\v9.0\
C:\Program Files\Reference Assemblies\Microsoft\VSTA30\v8.0\
C:\Program Files\Reference Assemblies\Microsoft\VSTA30\v10.0\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Visual Studio Tools for Office\PIA\Office15\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Visual Studio Tools for Office\PIA\Office14\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Visual Studio Tools for Office\PIA\Common\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Visual Studio Tools for Office\PIA\Office14\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Visual Studio Tools for Office\PIA\Office12\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Visual Studio Tools for Office\PIA\Common\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\Extensions\Microsoft\SharePoint\PublicAssemblies\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\ReferenceAssemblies\v4.0\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE\ReferenceAssemblies\v4.0\
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\Platforms\x64\
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\Platforms\Win32\
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\Platforms\Itanium\
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V110\
C:\Program Files (x86)\Reference Assemblies\Microsoft\VBPowerPacks\v10.0\
C:\Program Files (x86)\Microsoft Synchronization Services\ADO.NET\v1.0
C:\Program Files (x86)\Microsoft SQL Server Compact Edition\v3.5\Desktop
C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\15\TEMPLATE\WorkflowActivities\
C:\Program Files (x86)\Reference Assemblies\Microsoft\SharePoint15\
C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\15\ISAPI\
C:\Program Files (x86)\Microsoft SDKs\RIA Services\v1.0\Libraries\Server\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\ReportViewer\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE\PublicAssemblies\
C:\Program Files (x86)\Microsoft.NET\Primary Interop Assemblies\
C:\Program Files (x86)\Open XML SDK\V2.5\lib
C:\Program Files (x86)\Reference Assemblies\Microsoft\FSharp\2.0\Runtime\v4.0\
C:\Program Files (x86)\Reference Assemblies\Microsoft\FSharp\3.0\Runtime\v4.0\Type Providers\
C:\Program Files (x86)\Reference Assemblies\Microsoft\FSharp\3.0\Runtime\v4.0\
C:\Program Files (x86)\Microsoft SDKs\Expression\Extensions\FXG\Libraries\.NETFramework\v4.0\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\VSTSDB\
C:\Program Files (x86)\Microsoft ASP.NET\ASP.NET Web Pages\v2.0\Assemblies\
C:\Program Files (x86)\Microsoft ASP.NET\ASP.NET Web Pages\v1.0\Assemblies\
C:\Program Files (x86)\Microsoft ASP.NET\ASP.NET MVC 4\Assemblies\
C:\Program Files (x86)\Microsoft ASP.NET\ASP.NET MVC 3\Assemblies\
C:\Program Files (x86)\Reference Assemblies\Microsoft\Windows Identity Foundation SDK\v4.0\
C:\Program Files\Reference Assemblies\Microsoft\Windows Identity Foundation\v3.5\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\ReportViewer\
C:\Program Files\Reference Assemblies\Microsoft\Microsoft Identity Extensions\1.0\
C:\Program Files\Reference Assemblies\Microsoft\VSTO40\v9.0\
C:\Program Files\Reference Assemblies\Microsoft\VSTO40\v10.0\
C:\Program Files\Reference Assemblies\Microsoft\VSTA30\v9.0\
C:\Program Files\Reference Assemblies\Microsoft\VSTA30\v10.0\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Visual Studio Tools for Office\PIA\Office14\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Visual Studio Tools for Office\PIA\Office12\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Visual Studio Tools for Office\PIA\Common\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\Extensions\Microsoft\SharePoint\PublicAssemblies\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\VSSDK\VisualStudioIntegration\Common\Assemblies\v2.0\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\ReferenceAssemblies\v2.0\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE\ReferenceAssemblies\v2.0\
C:\Program Files (x86)\Reference Assemblies\Microsoft\VBPowerPacks\v10.0\
C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE\ReferenceAssemblies\v2.0\
C:\Program Files (x86)\Microsoft Synchronization Services\ADO.NET\v1.0
C:\Program Files (x86)\Microsoft SDKs\Microsoft Sync Framework\v1.0\Runtime\ADO.NET\V2.0\x64\
C:\Program Files (x86)\Microsoft SQL Server Compact Edition\v4.0\Desktop
C:\Program Files (x86)\Microsoft SQL Server Compact Edition\v3.5\Desktop
C:\Program Files (x86)\Reference Assemblies\Microsoft\SharePoint14\
C:\Program Files\Microsoft SDKs\Windows Azure\.NET SDK\2012-10\ref
C:\Program Files\Microsoft SDKs\Windows Azure\.NET SDK\2012-06\ref
C:\Program Files\Windows Azure SDK\v1.6\ref
C:\Program Files (x86)\Microsoft Visual Studio 10.0\ReportViewer\
C:\Program Files (x86)\Common Files\Microsoft Shared\MSEnv\PublicAssemblies\
C:\Program Files (x86)\Microsoft Chart Controls\Assemblies
C:\Program Files (x86)\Reference Assemblies\Microsoft\FSharp\2.0\Runtime\v2.0\
C:\Program Files (x86)\Microsoft SDKs\Microsoft Sync Framework\v1.0\Runtime\x86\
C:\Program Files (x86)\Reference Assemblies\Microsoft\FSharp\3.0\Runtime\v2.0\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Blend\
C:\Program Files (x86)\Microsoft Visual Studio 11.0\Blend\
C:\Program Files (x86)\Microsoft ASP.NET\ASP.NET MVC 2\Assemblies\
C:\Program Files (x86)\Microsoft ASP.NET\ASP.NET MVC 1.0\Assemblies\
C:\Program Files\Microsoft SDKs\Windows Azure\.NET SDK\2012-10\ref
C:\Program Files\Microsoft SDKs\Windows Azure\.NET SDK\2012-06\ref
C:\Program Files\Windows Azure SDK\v1.6\ref
C:\a\src\VpUserControls\Views\Navigation\DimensionTreeView.xaml(13,26): error MC3072: The property 'Bind.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 13 Position 26. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\a\src\VpUserControls\Views\Navigation\NavigationBarView.xaml(13,33): error MC3072: The property 'View.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 13 Position 33. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\a\src\VpUserControls\Views\Tools\ToolBarView.xaml(22,28): error MC3072: The property 'Bind.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 22 Position 28. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\a\src\VpUserControls\Views\Workspace\DimensionBarsView.xaml(11,19): error MC3072: The property 'Bind.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 11 Position 19. [C:\a\src\VpUserControls\VpUserControls.csproj]
Done Building Project "C:\a\src\VpUserControls\VpUserControls.csproj" (default targets) -- FAILED.
Done Building Project "C:\a\src\VP\VP.csproj" (default targets) -- FAILED.
Done Building Project "C:\a\src\ValuePlan.Client.sln" (default targets) -- FAILED.
Build FAILED.
"C:\a\src\ValuePlan.Client.sln" (default target) (1) ->
"C:\a\src\VP\VP.csproj" (default target) (2) ->
"C:\a\src\VpUserControls\VpUserControls.csproj" (default target) (3) ->
(ResolveAssemblyReferences target) ->
C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Microsoft.Common.targets(1578,5): warning MSB3245: Could not resolve this reference. Could not locate the assembly "Caliburn.Micro". Check to make sure the assembly exists on disk. If this reference is required by your code, you may get compilation errors. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Microsoft.Common.targets(1578,5): warning MSB3245: Could not resolve this reference. Could not locate the assembly "System.Windows.Interactivity". Check to make sure the assembly exists on disk. If this reference is required by your code, you may get compilation errors. [C:\a\src\VpUserControls\VpUserControls.csproj]
"C:\a\src\ValuePlan.Client.sln" (default target) (1) ->
"C:\a\src\VP\VP.csproj" (default target) (2) ->
"C:\a\src\VpUserControls\VpUserControls.csproj" (default target) (3) ->
(MarkupCompilePass1 target) ->
C:\a\src\VpUserControls\Views\Navigation\DimensionTreeView.xaml(13,26): error MC3072: The property 'Bind.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 13 Position 26. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\a\src\VpUserControls\Views\Navigation\NavigationBarView.xaml(13,33): error MC3072: The property 'View.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 13 Position 33. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\a\src\VpUserControls\Views\Tools\ToolBarView.xaml(22,28): error MC3072: The property 'Bind.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 22 Position 28. [C:\a\src\VpUserControls\VpUserControls.csproj]
C:\a\src\VpUserControls\Views\Workspace\DimensionBarsView.xaml(11,19): error MC3072: The property 'Bind.Model' does not exist in XML namespace 'http://www.caliburnproject.org'. Line 11 Position 19. [C:\a\src\VpUserControls\VpUserControls.csproj]
2 Warning(s)
4 Error(s)
Time Elapsed 00:00:18.83
Anyone have a similar problem or am I reading the log wrong and misunderstanding what's going on here.
EDIT
I'm thinking there is a possibility that the NuGet.targets file might be incorrectly set for hosted build. In the RestoreCommand part there is this -o modifier that some have reported is out of place.
<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup>
<SolutionDir Condition="$(SolutionDir) == '' Or $(SolutionDir) == '*Undefined*'">$(MSBuildProjectDirectory)\..\</SolutionDir>
<!-- Enable the restore command to run before builds -->
<RestorePackages Condition=" '$(RestorePackages)' == '' ">false</RestorePackages>
<!-- Property that enables building a package from a project -->
<BuildPackage Condition=" '$(BuildPackage)' == '' ">false</BuildPackage>
<!-- Download NuGet.exe if it does not already exist -->
<DownloadNuGetExe Condition=" '$(DownloadNuGetExe)' == '' ">false</DownloadNuGetExe>
</PropertyGroup>
<ItemGroup Condition=" '$(PackageSources)' == '' ">
<!-- Package sources used to restore packages. By default will used the registered sources under %APPDATA%\NuGet\NuGet.Config -->
<!--
<PackageSource Include="https://nuget.org/api/v2/" />
<PackageSource Include="https://my-nuget-source/nuget/" />
-->
</ItemGroup>
<PropertyGroup Condition=" '$(OS)' == 'Windows_NT'">
<!-- Windows specific commands -->
<NuGetToolsPath>$([System.IO.Path]::Combine($(SolutionDir), ".nuget"))</NuGetToolsPath>
<PackagesConfig>$([System.IO.Path]::Combine($(ProjectDir), "packages.config"))</PackagesConfig>
<PackagesDir>$([System.IO.Path]::Combine($(SolutionDir), "packages"))</PackagesDir>
</PropertyGroup>
<PropertyGroup Condition=" '$(OS)' != 'Windows_NT'">
<!-- We need to launch nuget.exe with the mono command if we're not on windows -->
<NuGetToolsPath>$(SolutionDir).nuget</NuGetToolsPath>
<PackagesConfig>packages.config</PackagesConfig>
<PackagesDir>$(SolutionDir)packages</PackagesDir>
</PropertyGroup>
<PropertyGroup>
<!-- NuGet command -->
<NuGetExePath Condition=" '$(NuGetExePath)' == '' ">$(NuGetToolsPath)\nuget.exe</NuGetExePath>
<PackageSources Condition=" $(PackageSources) == '' ">#(PackageSource)</PackageSources>
<NuGetCommand Condition=" '$(OS)' == 'Windows_NT'">"$(NuGetExePath)"</NuGetCommand>
<NuGetCommand Condition=" '$(OS)' != 'Windows_NT' ">mono --runtime=v4.0.30319 $(NuGetExePath)</NuGetCommand>
<PackageOutputDir Condition="$(PackageOutputDir) == ''">$(TargetDir.Trim('\\'))</PackageOutputDir>
<!-- Commands -->
<RestoreCommand>$(NuGetCommand) install "$(PackagesConfig)" -source "$(PackageSources)" -o "$(PackagesDir)"</RestoreCommand>
<BuildCommand>$(NuGetCommand) pack "$(ProjectPath)" -p Configuration=$(Configuration) -o "$(PackageOutputDir)" -symbols</BuildCommand>
<!-- Make the build depend on restore packages -->
<BuildDependsOn Condition="$(RestorePackages) == 'true'">
RestorePackages;
$(BuildDependsOn);
</BuildDependsOn>
<!-- Make the build depend on restore packages -->
<BuildDependsOn Condition="$(BuildPackage) == 'true'">
$(BuildDependsOn);
BuildPackage;
</BuildDependsOn>
</PropertyGroup>
<Target Name="CheckPrerequisites">
<!-- Raise an error if we're unable to locate nuget.exe -->
<Error Condition="'$(DownloadNuGetExe)' != 'true' AND !Exists('$(NuGetExePath)')" Text="Unable to locate '$(NuGetExePath)'" />
<SetEnvironmentVariable EnvKey="VisualStudioVersion" EnvValue="$(VisualStudioVersion)" Condition=" '$(VisualStudioVersion)' != '' AND '$(OS)' == 'Windows_NT' " />
<DownloadNuGet OutputFilename="$(NuGetExePath)" Condition=" '$(DownloadNuGetExe)' == 'true' AND !Exists('$(NuGetExePath)')" />
</Target>
<Target Name="RestorePackages" DependsOnTargets="CheckPrerequisites">
<Exec Command="$(RestoreCommand)"
Condition="'$(OS)' != 'Windows_NT' And Exists('$(PackagesConfig)')" />
<Exec Command="$(RestoreCommand)"
LogStandardErrorAsError="true"
Condition="'$(OS)' == 'Windows_NT' And Exists('$(PackagesConfig)')" />
</Target>
<Target Name="BuildPackage" DependsOnTargets="CheckPrerequisites">
<Exec Command="$(BuildCommand)"
Condition=" '$(OS)' != 'Windows_NT' " />
<Exec Command="$(BuildCommand)"
LogStandardErrorAsError="true"
Condition=" '$(OS)' == 'Windows_NT' " />
</Target>
<UsingTask TaskName="DownloadNuGet" TaskFactory="CodeTaskFactory" AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.v4.0.dll">
<ParameterGroup>
<OutputFilename ParameterType="System.String" Required="true" />
</ParameterGroup>
<Task>
<Reference Include="System.Core" />
<Using Namespace="System" />
<Using Namespace="System.IO" />
<Using Namespace="System.Net" />
<Using Namespace="Microsoft.Build.Framework" />
<Using Namespace="Microsoft.Build.Utilities" />
<Code Type="Fragment" Language="cs">
<![CDATA[
try {
OutputFilename = Path.GetFullPath(OutputFilename);
Log.LogMessage("Downloading latest version of NuGet.exe...");
WebClient webClient = new WebClient();
webClient.DownloadFile("https://nuget.org/nuget.exe", OutputFilename);
return true;
}
catch (Exception ex) {
Log.LogErrorFromException(ex);
return false;
}
]]>
</Code>
</Task>
</UsingTask>
<UsingTask TaskName="SetEnvironmentVariable" TaskFactory="CodeTaskFactory" AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.v4.0.dll">
<ParameterGroup>
<EnvKey ParameterType="System.String" Required="true" />
<EnvValue ParameterType="System.String" Required="true" />
</ParameterGroup>
<Task>
<Using Namespace="System" />
<Code Type="Fragment" Language="cs">
<![CDATA[
try {
Environment.SetEnvironmentVariable(EnvKey, EnvValue, System.EnvironmentVariableTarget.Process);
}
catch {
}
]]>
</Code>
</Task>
</UsingTask>

Answer 1

So I have managed to solve this myself. There must have been something wrong with one of my NuGet packages ( Caliburn.Micro 1.3.1 ) because when I updated that package the problem disappeared. I'm guessing there was something incorrect in the way that package looked for it's own assemblies but could not be sure because I'm not an expert on how NuGet packages work.
If someone has a similar problem I recommend looking at your packages, updating them and/or contact their developers asking if there could be a problem for automatic building.