Adding to Dmitri's comments, you might try using this custom repaint
manager to help detect any offending code:
(I've found it very illuminating in the past.)
http://weblogs.java.net/blog/alexfromsun/archive/2006/02/debugging_swing.html
https://swinghelper.dev.java.net/files/documents/4699/121607/CheckThreadViolationRepaintManager.java
Typically issues like this are caused by doing something Swing-related
off the EDT. Make absolutely sure you aren't doing something like that.
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