Framerate is higher in fullscreen for the same reason that games have higher FPS when it's fullscreen; the computer is only rendering that program, nothing else, so your graphics card doesn't have to do anything but focus on that one program. When you switch to windowed mode, same as if you play WoW or anything else windowed, your computer has to render the game as well as your browser and Windows and any other programs you've got running, so FPS sucks.
I always run windowed because I'm usually always doing something else with
SL in the background, but I wish I didn't have to.