I have a very similar problem actually. It's shifted slightly to the right side when I have my monitor vertical and launch the game full screen. I have everything rotated in Windows, but the problem still happened even if I had the game rotate instead of the desktop.
I wasn't able to find a solution, but instead just used Howards wrapper to launch the game at a larger size, but not quite full screen. This means it's not as big as it could be and there's some black around it all - but better then part of the game not showing at all.
If you find a solution, I'd be interested to hear it. If it helps, the computer it's doing it on is Win 7, Intel graphics. A few years old.