I've had that same issue in the past on my HDTV, and it tends to be a centering issue, though only when I was using fullscreen. If I auto-adjusted the screen it'll correct itself in the game, but then back on my desktop the screen will be off-center the opposite direction. It was an odd occurrence, but I don't recall exactly how I fixed it, other than running games in Windowed~Fullscreen if they had it, or forcing my resolution through .ini editing.

Try a different resolution, or better yet use this borderless window script and see if that helps any.