I can confirm this bug exists on 11.10 ( upgraded from Natty ). Had the
same problem on Natty, was hoping it would get fixed with the upgrade
but it didn't. On a Thinkpad T410 with only the built-in trackpad. No
external mouse/trackpad. This is an extremely frustrating bug that
requires me to reboot everytime it happens. Mouse and keyboard have
different focus and they are locked in. This has happened in Terminal
and Firefox mainly. This is an extremely frustrating bug where only a
reboot seems to be the way out. These are the last few lines in
Xorg.0.log :

[ 77544.628] (II) intel(0): Printing DDC gathered Modelines:
[ 77544.628] (II) intel(0): Modeline "1440x900"x0.0  101.30  1440 1488 1520 
1834  900 903 909 920 -hsync -vsync (55.2 kHz)
[ 77544.628] (II) intel(0): Modeline "1440x900"x0.0  101.29  1440 1488 1520 
1904  900 903 909 1064 -hsync -vsync (53.2 kHz)
[ 77545.479] (--) SynPS/2 Synaptics TouchPad: touchpad found
[ 77560.007] (II) XKB: reuse xkmfile 
/var/lib/xkb/server-9A8405F3FE0A780485714A4B6DD41909C2CF9F83.xkm
[ 77571.436] (WW) SynPS/2 Synaptics TouchPad: Ignoring new tracking ID for 
existing touch.
[ 78550.305] [mi] EQ overflowing. The server is probably stuck in an infinite 
loop.
[ 78550.322] 
Backtrace:

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https://bugs.launchpad.net/bugs/375905

Title:
  Mouse focus gets stuck over control objects

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