Description of problem: Given a panel with both autohide enabled, and a "Window List"[?] tray[?] with "Always group windows" selected, after selecting a menu-entry in a grouped window menu the panel forgets to autohide. (a menu entry might be from having multiple firefox windows open) A work around is to wave the mouse over the non-hiding panel.
Still present in FC6/FC7 and also reported upstream in http://bugzilla.gnome.org/show_bug.cgi?id=134563
Okay, let's let this trickle in from upstream.