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Yep. Now I see it. You're right. If I have OmniFocus minimized, there is no additional transparent window, but if OmniFocus is not minimized, then I get a transparent window. When I move my mouse over to the transparent window, I get the blue background to appear. I never noticed before simply because I was expecting the blue window to be there regardless of where the mouse was.

Very strange. Now I have to reverse my original position a bit and wonder if more people have this issue but either don't realize it or don't know how to get the blue box to display.

*shrug*

Luckily it's not an issue for me as I don't use Exposé.