Xcode failing to update binary - ios

I'm experiencing a very confusing issue with Xcode. It started when the debugger started skipping over some lines and stopping at the wrong lines on breakpoints. I tried adding NSLogs, but they weren't having any effect.
I restarted Xcode and did a clean build, and now no breakpoints fire anywhere, and NSLogs don't work either, even in -applicationDidFinishLaunchingWithOptions:. I've made sure that the current scheme is in Debug mode, so I don't know why this would be happening.
Has anyone else experienced something similar?
EDIT: Logs that were present before I started having this issue still work, but no new ones.

#Jumhyn, You should write the solution then by yourself and accept that answer and close it or accept this answer saying ... TRY TO RESTART YOUR COMPUTER :)

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Starting to get upset here, anyone who has the faintest idea of what could be wrong here?
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remove all breakpoints.
make sure you are not sharing breakpoints
in repository ;), check your git ignore file if needed, check data in
git.
add exception break point to all Objective-C Exceptions
run the project
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Edit2: It's not just user error; I can see the log messages from the new project with the copied files (see image). They just don't show in the old project when I run it.
Maybe you're not opened a Console in XCode 5, it seems, you're trying see a logs in member console.
Try click at here and you will see console with "All Output" option:
As noted in the comment by #combinatorial, I had a debug statement hidden (so cleverly that I fooled myself) in the pch file. Thanks so much for helping me nail that down!

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I realize that this is scant on details, but as I said, I'm not sure how to pinpoint the piece of code that's causing this error using XCode, otherwise I'd just debug this myself. If there's any extra information I can provide, let me know.
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chris
By console do you mean Output section? Could you try with a little app with only an NSLog to see if there's any change?

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