My first guess is that your code is calling AppKit unsafely from a background thread. But it sounds like your other thread only does calculations. Any other threads that might be making AppKit calls?
Second guess: something throwing an exception for some reason. Check the console output for any exception logs. Set a symbolic breakpoint at objc_exception_throw (on 10.5) or NSRaiseError (10.4) and see if it gets hit.
—Jens
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