I recently started running into the same problem.   In terms of
differences from what was posted before:

 - I was using the FGLRX driver.   I've uninstalled it -- I'll post back
if that solves my problem.

 - alt-tab does work

 - visual effects are set to "none"

 - logging in and logging out may or may not fix the problem

 - Some app (I'm not sure which) gave a warning "GtkMenu failed to grab
the pointer"

-- 
Mouse clicks stop working sporadically
https://bugs.launchpad.net/bugs/41301
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