When I use Fn-F7 to cycle between various configurations, gnome-display-preferences seems to not always get the message... E.g. I cycle to one of the cloned modes; the displays are clearly cloned, and xrandr reports: VGA1 connected 1280x1024+0+0 (normal left inverted right x axis y axis) 338mm x 270mm LVDS1 connected 1680x1050+0+0 (normal left inverted right x axis y axis) 331mm x 207mm Yet, gnome-display-properties shows only the laptop panel, and the cloned checkbox is unchecked. If I click on the laptop panel, the external monitor 'jumps out' from underneath it and the display looks like an on-top configuration now.
This appears to work correctly now.