This also happens to me when running in fullscreen. It seems like a global problem. You can manually set the resolution to your monitor resolution in the options menu. Although this makes it windowed, it's as close as it gets. If this problem appears in windowed mode, give a shout.
This problem might be because the cursor sometimes gets disoriented in fullscreen in several games, but the ingame cursor is located about 150px lower than the original Windows cursor. I'm not sure what this is caused, but my best guess is that it's because of the toolbar, or because of general monitor disorientation.
Lots of fancy words there, but I'm sure you can suck some sense out of it.