Bug#770979:

[Nathaniel Smith]

I also frequently experience what sounds like the same bug (clicks
going "right through" a fullscreen Iceweasel or fullscreen game and
being received by whatever is underneath; keyboard events are
delivered correctly). For me, though, it happens with fullscreen
applications on my single screen -- no multi-monitor setup required.

-- 
Nathaniel J. Smith
Postdoctoral researcher - Informatics - University of Edinburgh
http://vorpus.org