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.

-- 
[lucid] compiz-gnome broken because of metacity update
https://bugs.launchpad.net/bugs/558998
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