Comment 14 for bug 80343

I think the problem is Gnome can be notified (I don't know how this actually happens, but that's not the point) or can "understand" a compositor is enabled only if it is included in the windows manager. xcompmgr does all of its work indirectly, so when windows have already been created; that's probably why you don't get real transparency with gnome-terminal, and that's probably why the logout dialog still fades, locking the screen: in fact with a compositor-enabled wm the logout dialog does not have any background shade (I don't understand why gksudo worls, though).

solution? Dunno. This should be forwarded upstream. In the meantime I found using xfwm4 is fair enough