Comment 27 for bug 558998

After reinstalling most of the system, I tried logging in in GNOME safe mode, and metacity was running correctly. Big clue that it was something to do with the GNOME session, and I remembered I'd stored various startup applications.

So if starting metacity on the command line as above and then going to System > Preferences > Startup Applications > Options tab > click on "Remember Currently-running Application" and tick "automatically remember" seemed to work.

So this isn't apparently related to the compiz-gnome package, but to the upgrade process and its effect on the saved session. Might be the same as bug 563171 and/or bug 560065 which don't mention compiz-gnome.