I never have been able to get the 5040x1050 mode to work in Vista because of its know issue
Yeah this is always odd and frustrating because I had it working on Vista.
I tried swapping the displays, but what ever monitor has the right display, has the same flickering.
Have you updated the TH2G to the latest firmware version? My firmware version (which may not be the latest, worth checking online) is 2.3.40 (you can find this info by opening the Matrox PowerDesk and going to the About page).
The only other thing I can think of is that something hasn't saved properly in the profile, may be worth deleting all the profiles saved in PowerDesk and recreating them?