Happens for me too, but only before gnome-panel is fully loaded. While logging in to gnome a popup indicating limited diskspace appears partly out of view in the lower right corner.
-- popup notify is screwed up if panel is not on top https://launchpad.net/bugs/35005 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs