Can confirm this for 9.10 install CD and after 10.4 upgrade. Also, it
appears on Gentoo.

ALT-F2 and "metacity --replace" fixes this for a short time.
Removing wacom and synaptics input drivers doesn't help.

Configuration:

Desktop system with Intel motherboard and Pentium IV.
Video: 00:02.0 VGA compatible controller: Intel Corporation 82865G Integrated 
Graphics Controller (rev 02)
USB wireless mouse and keyboard, additional PS/2 keyboard.
Linux magic 2.6.32-22-generic #33-Ubuntu SMP Wed Apr 28 13:27:30 UTC 2010 i686 
GNU/Linux
xorg-server 2:1.7.6-2ubuntu7

Issue seems to be connected with hardware uptime (warm restart fixes it
for a short while when power-cycling fixes it for longer time).

-- 
Focus gets stuck to a window - impossible to select other windows
https://bugs.launchpad.net/bugs/362359
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