After many experiments...

it seems to be xinerama bug in xorg-server-1.6.0 - and yes, xinerama is
activated even if you use only one display output. and yes - it is
build-in into xorg-server, and CAN'T be deactivated (tried every
possible option in xorg.conf)

The only solution, which works for me is to DOWNGRADE xorg-server to the 
version shipped in Intrepid Ibex, see this guide:
http://dailyvim.blogspot.com/2008/12/ubuntu-downgrading-xorg.html
(just replace "hardy" with "intrepid" while adding sources into 
/etc/apt/sources.list)

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