Wait...fullscreen gives better framerate? I recently upgraded to a Radeon HD6850 and play in windowed and while it maintains perfect fps for the most part, there are sometimes spots in areas where the fps will take a hit randomly. Could this be why? Or is that just because of the poor optimization of the game?
Nothing to do with optimization. The game (or any game for that matter) is not given exclusive access to the display in windowed mode. Think about the OS trying to process the other windows/background on the same screen and you won't be surprised that there will be a FPS hit.