With help from Longinus00 on IRC I have figured out what is happening
here and why the workaround actually works.

The problem is the gconf plugin is getting loaded via command line. As
of the first compiz 0.8.3 packages plugins loaded from command line
cannot be disabled, ever. Since something is adding gconf to the command
line and ccp is already there the two plugins fight and they both lose,
neither one gets to save your settings. But what is adding gconf to the
command line?

If you have every switched WMs in older versions of Ubuntu the key
/desktop/gnome/session/required_components/windowmanager will still be
set to "gnome-wm" since we can't change keys for users. gnome-wm does
start compiz with gconf and thus we get this bug. This is why switching
to metacity and back to compiz via Appearance Properties fixes the
problem, it sets this key to "compiz" as it should be.

gnome-wm seems to have some code that is supposed to detect this case
and update the key for you but for whatever reason it is obviously not
working. Moving bug to gnome-session package since that is where gnome-
wm is located.

** Package changed: compiz (Ubuntu Karmic) => gnome-session (Ubuntu
Karmic)

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keybindings not remembered on reboot
https://bugs.launchpad.net/bugs/430981
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