This is a well complained issue, when Filemaker is using a lot of CPU, it "blocks" Mac OS X Gui, by sticking frontmost. Other app can't go frontmost, Filemaker can't get in the background.
It often happens after committing database structure changes (but not only).
This bug is there for years with all Filemaker an mac os x versions since I can recall, no i just filmed it with my iPhone. Filemaker is the only mac application behaving like that. It's time filemaker became a good Mac OS X citizen
Here's the movie, I hope it will entice FMI to fix that once for all