I think this is to do with the way we switch the panel configuration, gconf doesn't always merge the changed properly, and that leaves gnome-panel in an "in-between" state.
I've been informed of another way to implement the config switching which doesn't involve changing gconf in a huge way, and should solve this problem. I'm working on rewriting desktop-switcher to accommodate this change.
I think this is to do with the way we switch the panel configuration, gconf doesn't always merge the changed properly, and that leaves gnome-panel in an "in-between" state.
I've been informed of another way to implement the config switching which doesn't involve changing gconf in a huge way, and should solve this problem. I'm working on rewriting desktop-switcher to accommodate this change.