If the window you select is smooth as silk and the rest are choppy its because you have /console maxfpsbk set low. Either the program you're using to multibox (keyclone, etc) is setting that for you (most likely) or you set it yourself.

Ideally you WANT the windows that aren't active to be slower otherwise your video card probably won't be able to keep up. I usually set my "background" windows to 10fps and load them up behind the main window so I don't even see them. If I bring one to the foreground it speeds up anyway so its not a big deal.