Disappearing/Dysfunctional Menus under OS X.3

I turned on the Mac OS X menus with IntelliJ 3.0.5 under 10.3 and it looks almost like a native app! BUT, every so often the menus completely disappear (except for the IntelliJ menu) and will reappear if I click on where they should have been. More critically, occassionally, the menus just stop working altogether. They are there, but they just don't do anything if I click on them.

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