I can't really offer a solution, just some input:
I'm using a dual-head EVGA nVidia 9500 GT. Dual screens in Windows is a bit wonky, I think. I've only used it with Win7, though. Some games won't even run unless I disable the second screen, with other games I experience things similar to what you mentioned.
Using Twinview in Linux, Tribes crashes when I try to run it full screen unless I have Wine running a virtual desktop. (Allows for OpenGL in a window, it's rather nice. But GG/IA's new Tribes version will make that possible anyway.) It doesn't have any issues with the screen going off/on, stuff being improperly positioned, or the like.