In previous versions of Red Hat Linux, clicking on a window would bring it to the front of other windows which overlapped it. That no longer works -- you can't bring a window to the front with the mouse unless you can see its title bar or a border. This is surprisingly painful -- I hadn't realised how often I used this :) I can't see any way to enable it again.
I can't reproduce this with the latest Rawhide Metacity. What version are you running? And what applications are you testing with?
Every version of metacity which has been in Severn since I reported the bug, and all applications. Hitting Alt-Button1 brings a window to the front; just Button1 doesn't.
Moved to http://bugzilla.gnome.org/show_bug.cgi?id=115072