>>From the Jprofiler monitoring, it shows the PermGen memory area is getting filled up
I rather doubt that this is true. The permgen always runs at 99% full; seeing that is not a cause for alarm. If there was not enough room to add addtional classes, you would get an OOME.
Radoslav's recommentation is the best: take a Java thread dump (not a Linux thread dump) and examine the stack traces for the threads that are "stuck".