I have the same issue.  The main difference is that I'm using a Matrox
G550 with xinerama instead of nvidia as everyone else here seems to be
using.  I've been running into the problem on average about once a day.
Restarting X fixes the problem.  I had been running Hardy for 6 months
with no problem on the exact same setup.

After reading this ticket yesterday, I opened an xev on each of my two
heads.  After loosing the ability to click and change focus I
experimented with those two xev windows.  It seems that when I move the
mouse around the screen0, the xev on screen1 starts showing events.
Before the problem, moving the mouse in the xev window produced
coordinates around 2080,600.  After the mouse problem started,  hovering
on the xev window didn't produce events, but moving around screen 0 at
location 800,600 did produce events and the events had the coordinates
800,600.  In other words the events seemed to be coming from a location
exactly one screen width ( in my case 1280 ) away from where they were
supposed to be.

Also, I noticed that the cursor changed from the usual pointer to the
text entry cursor on screen0 corresponding to the placement of windows
on screen1, again exactly one screen away.

Just for full disclosure, the xorg mga driver in intrepid is broken and
needs a patch to get xinerama working in the first place.  See bug
292214 for details. But after finding this ticket, I think my mga issues
are independent of this mouse issue.

-- 
X.org will intermittently stop responding to mouse clicks on Ibex with Xinerama
https://bugs.launchpad.net/bugs/296167
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