I don't think monitor's native has anything to do it. More likely a bunch of resolutions are broken right now, the game doesn't know where the screen edges are when running them.
None of these work right on my screen:
1280x960
1366x768
1400x1050
1440x900
1600x900
1680x1050
Well, you guys could also just add much better zoom scaling (with smoothing) and that would also be good.