Haven't loaded it yet (still downloading), but if this is a consistent issue, I hope this is something that can get resolved. I hate being stuck in-game because it will crash if I want to browse or answer an IM (I have Raptr but the overlay causes too many problems/crashes to be worth using).
Same here, Xsyon in windowed mode works fine with alt-tab. You'll quickly learn to aim your cursor a couple millimeters below what you're trying to click too