I really don't know how to move on from here. I don't think that you
need to start both compiz and metacity, it's one or the other. Starting
either one with --replace terminates the other if it's running, at least
that's my understanding.

The error in syslog regarding gnome-session might be related to one of
the Startup programs. Check to see if you have a Compiz entry there. I
don't think there should be one, actually. I don't have one, and Desktop
Effects is activated (on an Intel graphics card as well). I think the
choice of Window manager/decorator is made using the gconf key discussed
earlier.

What you describe might indicate a bigger problem with the overall
settings of your desktop, ie some gnome components seem unable to load
since the top panel and keyboard shortcuts doesn't work. If this is
because a faulty Compiz or the other way around I don't know. I would
suggest that you create a new user and test it out, and see if the
problems persists with that user. If not, then the problem most likely
is not with faulty packages but rather your settings configuration.

Possible solutions to that problem might be to remove more of the
settings folders, perhaps all related to the Gnome desktop environment.
This seems a bit extreme and possibly unsafe, you have to be careful to
save folders belonging to programs you do not wish to reset.

If you have problems even with a new user, then there must be some
packages that hasn't been installed correctly. A reinstallation of
compiz and desktop environment might do the trick, in that case start
from a recovery console and purge and reinstall the desired packages. I
don't know if that's the best praxis. You could try asking, or
searching, on Ubuntuforums.org which way is best to reinstall the
desktop environment, if nobody besides me decides to answer here :)

Important to note is that I also get the warning message regarding GLX
1.3 function when starting compiz with compiz --replace & in a terminal,
and my environment works just fine (fresh install though, but some
settings moved from earlier installation).

-- 
metacity and compiz aren't working properly at startup
https://bugs.launchpad.net/bugs/543097
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