In Windows, your desktop gets hardware 2d acceleration. The video card handles drawing much of the transparent areas and moving windows (with accel fully off, try moving a window, especially around a transparent area, and it will be slower). The thing it does that causes problems, I believe, is that most video goes through the video card to make it look nice and smooth (also, Radeons and Geforces have integrated MPEG1/2 decoding).

However, this will disable other acceleration. You'll have to move it back up to max to play games; but AFAIK, nobody has a clue why this stuff requires Explorer.