I think I am having a related problem as well with the same setup: one desktop over another. I have attached a screen shot. In my case, the lower portion of applications is hidden behind the lower gnome panel.
** Attachment added: "maximize-bug.png" http://launchpadlibrarian.net/27177091/maximize-bug.png -- maximized windows have titles covered by gnome-panel in twin view mode https://bugs.launchpad.net/bugs/375503 You received this bug notification because you are a member of Ubuntu Desktop Bugs, which is subscribed to gnome-panel in ubuntu. -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs