Fedora 10 ships with compiz, and launches it as: compiz --ignore-desktop-hints glib gconf
If the gconf /apps/compiz/general/allscreens/options/active_plugins key does not contain "gconf" as a value in the list, the gconf plugin will unload itself after setting core options and stop listening to gconf notify events. No plugin settings set with ccsm using the gconf backend will stick unless it's there (presumably added with gconf-editor). Furthermore, adding or removing an active plugin via ccsm will remove the "gconf" entry from active_plugins in addition to the plugin you removed (or added).
It seems like if you're overriding the active_plugins list from the command line, the gconf backend should ignore attempts to remove plugins specified there. Or at the very least, if the gconf plugin was loaded at all, it should implicitly add itself to the list if not already present.
This behaviour makes plugins with non-default configuration values fairly unusable in F10 without hackery.
Mass closure: This bug has been untouched for more than six years, and is not
obviously still valid. Please reopen this bug or file a new report if you continue to experience issues with current releases.