Here's a related question: Why does the -res flag in non-standard resolutions position the game in the upper-left corner of my screen instead of invoking the centering and black bands that my display uses for standard but non-native resolutions? E.g the monitor is 1680x1050, and set to 1024x768 the game will run centered with the black bands that my display uses... but at 1365x1024 or 1400x1050, it defaults to upper-left corner with no black banding.
It's annoying. I've tried both the nVidia scaling with locked aspect ratio and my monitor's built-in, which is the normal one I use. Both generate this behaviour, and it seems confined to FSO.