Why do my Swing application windows intermittently not close when the application exits?

Why are my Swing applications not closing when using Netbeans 6.5 on Ubuntu 8.10 with Sun JDK 6. Even the Netbeans tutorials downloaded from the Netbeans website do the same. When I close the application I’m left with a dead window. I then have to manually kill the process. It comes and goes, but I can’t figure out what triggers this behavior.

I have also run my applications from the command line terminal using openjdk (6b12-0ubuntu6.1) and sun-java (6-10-0ubuntu2), still no luck. I have noticed when running it through netbeans after trying to close it netbeans still shows the app as running and after manually killing the process my netbeans log prints “Java Result: 137”

Update – 4Mar: I have also tried upgrading to Sun JDK 6u12 and Netbeans 6.7m2. But still no luck.

Update – 4Mar: Ok, after further testing I found that this behavior starts as soon as I add JPA to my application. That makes explains why the JPA tutorial examples on the netbeans website also do the same. I have tried writing an ExitListener to first close the EntityManager but no luck yet. If I delete the EntityManager, Query and List from my Form Panel the applications closes properly again.