Comment 3 for bug 206259

Thanks for the hint with ~/.xsession-errors
The problem was, it was flooded with messages from evolution and rhythmbox, so I rebooted and here's the error message:

(gnome-appearance-properties:8841): GLib-CRITICAL **: g_array_free: assertion `array' failed
Attempted to unregister path (path[0] = org path[1] = freedesktop) which isn't registered
Attempted to unregister path (path[0] = org path[1] = freedesktop) which isn't registered
Attempted to unregister path (path[0] = org path[1] = freedesktop) which isn't registered

(gnome-appearance-properties:8841): GLib-CRITICAL **: g_array_free: assertion `array' failed
ERROR: Only administrators can use this function.

Full ~/.xsession-errors is attached. It also proves that the issue is only with gnome-appearance-properties because prior to the reboot, I set the gconfs key /desktop/gnome/applications/window_manager/default to /usr/bin/compiz and it worked, I had Compiz on startup.
Only after I used gnome-appearance-properties to switch it off and back on, Compiz wouldn't work.