The thing unclutter conflicts with is SDL's relative mouse input.  If you 
export SDL_MOUSE_RELATIVE=0
before running an SDL game, the mouse won't jump.  OTOH, an FPS like nexuiz 
will be unplayable because you won't be able to turn freely!  But this does 
confirm that it's SDL's relative mouse input that is broken by unclutter.

 So it has nothing to do with xserver-xorg-input-mouse


** Changed in: unclutter (Ubuntu)
Sourcepackagename: xserver-xorg-input-mouse => unclutter

** Description changed:

  I have this bug in Edgy with Nexuiz, Tremulous and Wormux, so i assume
  it is on a deeper level. SDL maybe?
  
  The mouse jumps around every second or so. Sometimes regularly to the
  center, but sometimes to other points. It looks like some kind of
  position reset or something. It happens fullscreen and windowed.
+ 
+ (summary of comments: It's unclutter's fault.  It interferes with SDL's
+ relative mouse input.  If you're seeing this bug and there isn't a
+ smarter unclutter released yet, just killall unclutter.)

-- 
Mouse jumps to center in (sdl?/opengl?) games
https://bugs.launchpad.net/bugs/61105
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