I've been experiencing severe mouse focus problems on and off when using the nvidia binary module.
Some searching on the net found anecdotes of similar problems.
(see last couple of comments)
Obviously it's hard to debug since I couldn't see an easy way to override an XGrabPointer (I'm not well versed in X, so there might be some blindingly obvious way to debug this). My current workaround is mainly right-clicking randomly till a menu pops up, which cures the pointer grab. If I'm lucky, the focus is to a window that I can close using the keyboard thus ungrabbing the pointer. If I'm unlucky, Alt-SysRq-K is the only option.
Linux kernel 2.6.30-rc6