Do you also have the problem, that you sometimes get a messy gnome-panel on your gnome powered Linux desktop after booting the system or adding another display to your configuration? Here's a quick fix for those situations.
Just restart gnome-panel:
$ killall gnome-panel
That should bring everything back to order. If not, try the hardcore way:
$ gconftool-2 --recursive-unset /apps/panel && killall gnome-panel &
This will reset your gnome-panels to the default values. However, you will have to add all your panel-shortcuts and programs again afterwards.