[Preface: I replied a bit too quickly. What I'm finding is not related specifically to clipping, I find that the Quick Entry window often appears behind other windows even just using the Quick Entry hot key.]
I too have this happening relatively regularly. I'm not sure what circumstances precipitate it, but it doesn't always happen, and my impression is that restarting OmniFocus fixes it (temporarily), though I haven't tested this rigorously.
I'll try to keep an eye out for what circumstances I might see this in, but I have one other piece of data that might help: Quicksilver B59 also suffers from this problem. There, it's actually worse, because the QS window shows itself in the center of the screen, an area which is almost invariably covered by some other window. At least my Quick Entry screen is off to one side, so I can see it peeking out from behind other windows.
This suggests to me that it's something more general than a bug in OmniFocus, but no matter where the underlying cause lies, it still interferes with my use of OF (and now QS) and I'd love to figure out how to make the problem go away.
(Mac OS 10.6.7, OF 1.9)
Last edited by paulhagstrom; 2011-04-20 at 05:09 AM..
Reason: not just clipping, also for regular use of Quick Entry