I know it sounds odd. Netbeans 3.6 (I know - old) tends to fall over if apps repeatedly terminate abnormally. I also noticed this behaviour more frequently after adding controllers. I wondered if there was a memory leak somewhere.
I found this
If you run out of memory, it could be that there are too many processes running simultaneously. This can happen if you run a program and it crashes but the process has not been terminated or if you omit the line System.exit(0);.
Periodically you can select View / Execution for a list of processes and right-click on each unnecessary process to terminate it(or exit NetBeans completely and then re-start).
So I could be wrong

Maybe something just keeled over. I'll do some more scientific testing.
Edit - Think I'm wrong

- I ran the app a good dozen times within Netbeans without hitting any problems. I think my earlier problems must have been purely down to app crashes during development destabilising Netbeans.