If you're getting FPS trouble when a window is hanging slightly over into the next monitor, that's purely a graphics bug. Back in the old days, not only could you not do this at all, you couldn't even run Direct3D surfaces on a secondary monitor. They eventually fixed that about a year after Win2k came out but the support is still very much reliant on the graphics drivers to support it well. You might be running into an issue with NVidia's Vista drivers there. Easy test is to swap the video card onto your old machine on XP and see if you get the same behavior. If not, then it's either Vista itself or the NVidia Vista drivers. If it happens on Xp as well, it's a general issue with the NVidia drivers.

Hope this helps.