Using the script from http://wiki.beryl- project.org/index.php/Install/Ubuntu/Edgy/XGL#Adding_an_Xgl_login_session , under "Shutdown and reboot buttons in GNOME" fixes the issue for me.
-- Incomplete logout options with XGL https://launchpad.net/bugs/36321 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs
