In my case when I was running on GF4 Ti4400, there would only be a few resolution working, and the others would either go in the black screen and I'd have to reboot in safe mode to switch it back, or they would be flickering like mad. I supposed different TV/Vid Card combo might result in different set of working res. Generally it is best I guess to set the game res to which ever res is working under the desktop environment, so you know at that res the refresh rate is matching with the TV. In my case with Ti and Sony 50WE620 GWIII, my 720 works but has overscan so I had to use the nVidia underscan option to get 1177x662. My 800x600 works, my 640x480 works, and that's about it. My 1024x768 flickers, so does my 1080 res. And all the rest doesn't work at all. This is without resorting to any other app like powerstrip. And all these apply to any application that runs these res. With my new 6600GT I have no flickering problem at all in any res, only underscan and overscan, they can be adjusted accordingly, maybe this has to do with whatever TMDS that is different in the GF6 series card.
I guess my suggestion would be first find out whats working and set the game up accordingly. I don't know how to use powerstrip or nVidia's advance timing, so maybe someone else can help you out if you need to resort to that.
Best of luck.