X.org itself doesn't manage these config settings.  The layout is
actually done by the GNOME display preferences.

As to why compiz settings get reset, that sounds more like an issue with
compiz, so possibly you should file a second bug against it.  The gnome
guys would know better.

** Package changed: xserver-xorg-video-intel (Ubuntu) => gnome-control-
center (Ubuntu)

-- 
Compiz settings lost when extra monitor attached (intel driver)
https://bugs.launchpad.net/bugs/530304
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