I am running Ubuntu 12.04. on a Lenovo Thinkpad T400. I connected an external monitor as a second display. The laptop stands under the external screen. The laptop has a native resolution of 1440x900 (16:10), the external monitor 1280x1024 (5:4). There are two graphic adapters: one internal Intel GMA 4500 MHD and an discrete ATI card. Currently, the integrated Intel is enabled.
I use the Display application to arrange the position of the monitors so it look like this:

The problem:
Whenever I restart my computer the configuration gets lost. First, the displays are mirrored instead of extended. I have to press Fn + F7 two times to switch to extended mode. Second, the Display settings still look like this:

I know this worked once when I was running Ubuntu 10.10. I cannot tell since when it does not work. Do you know how I can permanently store the settings?