The most common cause of this problem is when an application is redeployed "hot" in Tomcat6, and there are indications that it's actually somewhat of a bug. Certainly I'd never heard of it in Tomcat5.
The heap is not the PermGen space. There's a separate config parameter in the Oracle/Sun JVM for PermGen space. However, I played around with that parameter about 2 weeks ago to no avail. I'm hoping Tomcat7 is going to do better.
An IDE is no substitute for an Intelligent Developer.