I'd like to note that I am affected by this issue as well. However I did
find a work around on my system (mint 9, ubuntu 10.04).

Right after the symptoms begin to pop up and my computer freezes except
for the one window, I press ctrl alt backspace, drop back into log in
screen, log back in, and usually the mouse works fine after this. If i
disconnect and reconnect the mouse, the issue returns. Also, as I recall
(it's been awhile since I tried to fix it myself) if I fiddle with the
mouse settings using xinput the issue returns again.

-- 
Madcatz Cyborg R.A.T. 7 focus issues
https://bugs.launchpad.net/bugs/615892
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