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Did you ever figure this one out? I seem to have the same problem. I am guessing that the javahelp starts up a thread that is not marked as 'daemon'. The thread is left alive and the application will not shut down.
Did you ever get a solution?
Primary window gets never disposed (according to jhug.pdf), this is the reason. See here to check Swing behaviour.
You should find a way to get it and dispose it.
Otherwise adding a new event to the EventQueue to just stop the EDT may suffice (I never had such a problem).
If you can't figure out a JH solution you might try to ask in the Swing forum (I'd suggest waiting a couple of days in order to avoid cross-posting).