For other reasons I recently gutted my PC and am running a fresh install of Win7 and BMS. Now I get better fps and smoother panning in full screen mode, and it is much worse in windowed mode. This is better for the 2d interface because I am using a 4k TV as a display, but it makes the issue much more mysterious. Some setting I had in the past was causing the problem in full screen mode and I do not know what it was.