I hit a similar problem, essentially Visual Effects (compiz) are not
working after upgrade to 9.04.

Prior to 9.04 I was using the ATI driver.  Since that's not been
possible after the upgrade, I'm now using the open source radeon driver,
but although that worked ok, any attempt to re-enable desktop effects
gave me the message that effects could not be enabled.

Attempting to launch compiz from the command line gave me:

      $ compiz --replace
      Checking for Xgl: not present.
      xset q doesn't reveal the location of the log file. Using fallback 
/var/log/Xorg.0.log
      Detected PCI ID for VGA:
      Checking for texture_from_pixmap: not present.
      Trying again with indirect rendering:
      Checking for texture_from_pixmap: present.
      Checking for non power of two support: present.
      Checking for Composite extension: present.
      Checking screen 1Comparing resolution (2560x1024) to maximum 3D texture 
size (4096): Passed.
      Checking for Software Rasterizer: Not present.
      Checking for nVidia: not present.
      Checking for FBConfig: present.
      running under gnome seesion, checking for gnomecompat
      Checking for Xgl: not present.
      /usr/bin/compiz.real (video) - Warn: No 8 bit GLX pixmap format, 
disabling YV12 image format
      Starting gtk-window-decorator

After going on the compiz irc channel, I was asked to disable window
decoration in ccsm.  Doing that did allow me to turn effects back on,
although checking ccsm again reveals that window decoration is enabled
again.

Now, while this was an upgraded install, I'd had to wipe out all my
compiz settings to log on due to another bug.  So this was all happening
with the default compiz preferences.

-- 
cannot set "Visual Effects" to Extra after upgrade to 9.04
https://bugs.launchpad.net/bugs/368766
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