So Michael Vogt has just released a new version of compiz package which 
blacklist some ati mobility cards (X300,X600,X700).
I think this was the right way to go since the problem cannot be easily fixed. 
Thank you, Michael

compiz (1:0.6.0+git20071008-0ubuntu1) gutsy; urgency=low
 .
   * New git snapshot:
     - properly fix bug to never stack under the desktop window (LP: #147943)
     - fixes in the internal stack representation, this fixes the issue
       that sometimes windows are put over or under panel windows
   * debian/patches/026_fix_stacking:
     - dropped, now part of upstream
   * debian/patches/028_compiz_manager_blacklist:
     - blacklist ati mobility X300,X600,X700 freezes (LP: #115283)

-- 
X freezes when compiz is enabled on ATI cards
https://bugs.launchpad.net/bugs/108527
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