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I found that some folders in .config had been created with root
permissions somehow (perhaps through launching 'sudo geany' early on in
the life of this desktop to edit a config file - I can imagine this
would be an unintended consequence of the first run of some gnome
program being sudoed).

Having found the unusual permissions, I recently changed all such
folders in my home directory from root ownership to my user's ownership
- an example being the .config/gtk-2.0 folder. I then proceeded to
reconfigure compiz. As of recent hours, changes made through CCSM seem
to endure between sessions and DBus and Command can run and do not crash
compiz. These issues may be related or not.

** Changed in: compiz (Ubuntu)
       Status: New => Invalid

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https://bugs.launchpad.net/bugs/1168774

Title:
  Compiz Configuration changes transient, create unstable compiz

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