I've not been able to pin point exactly what causes this bug, but it is most annoying.
I tend to switch applications a lot, and minimize idea frequently. I've noticed that sometime upon returning to IDEA focus doesn't completely return. This also happens I believe when several of the dialog boxes that IDEA generates change the focus of the app.
Essentially, the application menu becomes useless. Every menu option is grayed out and can't be used. The IDEA window menu continues to work however. But key mappings that exist in the application menu as well as the IDEA menus stop working. Command + Q for instance stops working and the only way to close IDEA is to use the File menu and click exit. The rest of IDEA works as expected and is fully functional.
This problem just seems to get even worse if you hack the Info.plist file and set the apple.laf.useScreenMenuBar property to true. In this case the whole IDEA menu system becomes unusable, the only way to exit is by clicking the "Close Window" control button in the top corner of the app window (this only works in more recent builds 1117 that i know of). Or by using force quit.
Like I said in the beginning, I am not sure what is the cause of this so this post is really just to find out if anyone else is experiencing the same problems on OS X.
I am currently running 10.3.2 with the ADC DP2 release of Java 1.4.2_03.