I don't know if this is related, but when I upgraded some GNOME packages a while back, the menus got changed up a lot. I think I got the GNOME 2.10 menu arrangement, while still using other GNOME packages from 2.8. So I lost my custom menu entries, and the ability to edit said menus, but a lot of KDE apps now show up in my GNOME menus. I assume when 2.10 makes it into testing that will help. :)