Yeah, if it helps, I'd like to mention that WinUAE has gone through several stages of development where various releases would "break" functionality of certain games. There were a few releases of WinUAE that I had that simply caused Speedball 2 to either crash or, most recently, have a line of graphics jump around on the screen through the entire game.
The most recent version of WinUAE doesn't seem to have any problems with it, though. Maybe you're using an older version?