I was having an issue in battlefield 3, the only way I could make the mouse pointer line up with the in game menus was to point it at a location far down and to the right of the actual buttons. It was annoying me to death.
Anyhow the first solution was to disable all visual features in windows, but that's lame.
I finally discovered that by right clicking the program icon - properties - compatibility and ticking 'disable display scaling on high dpi settings' (pictured below) finally solved it.
I don't expect this is a very common problem, but I figure it has to be affecting someone else out there using high resolution settings so I thought I would share the fix.