Did they actually include a Metacity part? A lot of themes are made for GNOME 3 and don’t include parts that are useless on it. It’s possible that Compiz is more strict with the interpretation of the index.theme: i.e. if a theme declares a non-existent Metacity part, it will work just fine with Marco (I assume it’ll just keep the previously selected Metacity theme) but maybe Compiz will just not decorate the windows borders.
That’s just an hypothesis out of the blue, I guess we would need to check the problematic themes more thoroughly to see what causes the issue.