I've found a workaround here: http://bugs.debian.org/cgi-
bin/bugreport.cgi?bug=305992

Launching game this way prevents pointer jump:
export SDL_VIDEO_X11_DGAMOUSE=0 && urbanterror

** Package changed: ubuntu => xserver-xorg-input-mouse (Ubuntu)

** Bug watch added: Debian Bug tracker #305992
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=305992

-- 
In fullscreen apps mouse cursor jumps to bottom-right corner when I click
https://bugs.launchpad.net/bugs/441408
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which is subscribed to xserver-xorg-input-mouse in ubuntu.

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