Since I upgraded to 12.10, (Quantal) I have have all sorts of issues because apparently gnome is moving away from compiz and using something of their own, but I'm using cairo-session which uses gnome-session, ... Whatever anyway ubuntu-tweak isn't working completely for me and the stupid overlay tool bars kept reappearing. The command below disables them:
gsettings set com.canonical.desktop.interface scrollbar-mode normal
Another thing that's not persisting is window focus mode:
dconf write /org/gnome/desktop/wm/preferences/focus-mode \'sloppy\'
dconf write /org/gnome/desktop/wm/preferences/auto-raise false
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