What is wrong with these Tomcat database connection pooling configuration - connection-pooling

Question

From last two years on tomcat I am using this configuration for database connection pooling in tomcat
<Resource auth="Container"
driverClassName="com.mysql.jdbc.Driver"
logAbandoned="true"
maxActive="100"
maxIdle="30"
maxWait="10000"
name="jdbc/maindb"
password="xxxxx"
removeAbandoned="true"
removeAbandonedTimeout="60"
type="javax.sql.DataSource"
url="jdbc:mysql://localhost:3306/maindb?zeroDateTimeBehavior=convertToNull"
connectionProperties="useEncoding=true;"
username="sqladmin" validationQuery="select 1"/>
On production server, from last one month, with this configuration - suddenly tomcat stop responding to any requests. And results in timeout. There is no errors in logs, but as soon as I shutdown tomcat a huge amount of error log comes, which seems to show some kind of deadlock in database connections.
To rectify it, I used database connection pooling configuration from http://tomcat.apache.org/tomcat-8.0-doc/jdbc-pool.html . After using this configuration, now I face two problems, on production, either a table lock occurs even after using INNODB engine, or some queries start returning empty result set even when query is perfectly fine.
<Resource name="jdbc/maindb"
auth="Container"
type="javax.sql.DataSource"
factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
testWhileIdle="true"
testOnBorrow="true"
testOnReturn="false"
validationQuery="SELECT 1"
validationInterval="30000"
timeBetweenEvictionRunsMillis="30000"
maxActive="100"
minIdle="10"
maxWait="10000"
initialSize="10"
removeAbandonedTimeout="60"
removeAbandoned="true"
logAbandoned="true"
minEvictableIdleTimeMillis="30000"
jmxEnabled="true"
jdbcInterceptors="org.apache.tomcat.jdbc.pool.interceptor.ConnectionState;
org.apache.tomcat.jdbc.pool.interceptor.StatementFinalizer"
username="sqladmin"
password="xxxxx"
driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/maindb"/>
In case of first configuration, after shutting down tomcat following error logs start coming
04-Feb-2015 20:44:46.048 INFO [main] org.apache.catalina.core.StandardServer.await A valid shutdown command was received via the shutdown port. Stopping the Server instance.
04-Feb-2015 20:44:46.049 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-apr-8080"]
04-Feb-2015 20:44:46.100 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-apr-8009"]
04-Feb-2015 20:44:46.151 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
04-Feb-2015 20:44:46.157 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 81 instance(s) to be deallocated for Servlet [dispatcher]
04-Feb-2015 20:44:47.158 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 81 instance(s) to be deallocated for Servlet [dispatcher]
04-Feb-2015 20:44:48.160 INFO [localhost-startStop-2] org.apache.catalina.core.StandardWrapper.unload Waiting for 81 instance(s) to be deallocated for Servlet [dispatcher]
04-Feb-2015 20:44:48.260 INFO [localhost-startStop-2] org.springframework.context.support.AbstractApplicationContext.doClose Closing WebApplicationContext for namespace 'dispatcher-servlet': startup date [Tue Feb 03 18:26:26 UTC 2015]; parent: Root WebApplicationContext
04-Feb-2015 20:44:48.307 INFO [localhost-startStop-2] org.springframework.context.support.AbstractApplicationContext.doClose Closing Root WebApplicationContext: startup date [Tue Feb 03 18:26:24 UTC 2015]; root of context hierarchy
04-Feb-2015 20:44:48.310 INFO [localhost-startStop-2] org.springframework.scheduling.concurrent.ExecutorConfigurationSupport.shutdown Shutting down ExecutorService 'taskExecutor'
04-Feb-2015 20:44:48.329 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] is still processing a request that has yet to finish. This is very likely to create a memory leak. You can control the time allowed for requests to finish by using the unloadDelay attribute of the standard Context implementation. Stack trace of request processing thread:
sun.misc.Unsafe.park(Native Method)
java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
org.apache.tomcat.dbcp.pool2.impl.LinkedBlockingDeque.takeFirst(LinkedBlockingDeque.java:582)
org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:439)
org.apache.tomcat.dbcp.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:360)
org.apache.tomcat.dbcp.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:118)
org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1412)
com.myproj.dao.ConnectionPool.getConnection(ConnectionPool.java:41)
And in second case following error logs comes, while doing certain operation
22-Jan-2015 16:36:04.077 SEVERE [http-apr-8080-exec-2] com.myproj.dao.cart.impl.VisitorCartDaoImpl.addCartItem Lock wait timeout exceeded; try restarting transaction
java.sql.SQLException: Lock wait timeout exceeded; try restarting transaction
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:996)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3887)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3823)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2435)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2582)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2530)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1907)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2141)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2077)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2062)
at com.myproj.dao.cart.impl.VisitorCartDaoImpl.addCartItem(VisitorCartDaoImpl.java:96)
Is there anything wrong with the configuration or with the database? I am using MySQL 5.6 as the database and on production, mySQL is running on amazon RDS. And I am using tomcat 8.0.15