It doesn't seem to like dual screens when you do that though. Whenever I use windowed mode it keeps shunting the window between my two monitors, and it will do it whenever the game changes through say, a major option screen. It got so annoying I just stuck to full windowed mode and put up with the same stuff the OP describes.
Edit: Huh. I just went back to my steam library and removed the -popupwindow command and then put it back in to give it another try. Seems like it works better now. Neat.