I have this same issue and THINK I FOUND THE TRIGGER..

I have two different Nvidia's (PCIe) and 3 monitors.
I setup xinerama to link the displays, which is working great! Until once in a 
while my mouse isn't working as expected anymore.

When I run 
tail -f Xorg.0.log

I can see that the messages:
miPointerWarpCursor: Invalid input device pointer
miPointerUpdateSprite: Invalid input device pointer
miPointerConstrainCursor: Invalid input device pointer

start appearing once you hold a key (however not Shift).

Run tail -f and press some enters to get some white lines.
Now hold enter (to get more white lines even faster...) You will see the 
messages will also appear immediately! And of course your mouse cursor is out 
of sync.


Maybe this can help to fix the problem.

-- 
[multi screen] mouse position sometimes wrong
https://bugs.launchpad.net/bugs/363375
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