I see.
I guess it has something to do with the signals for sound - how the soundcard (or on-board chip) is adressed, IRQs ? DMA ? I don't know, but the "stuttering" or "distortedness" sounds to me as if the priority of the signals is set to a lower level than for a non-windowed game.
I remember that for DOS games you could set (right-klick on exe file) several options, for example interrupts, and maybe even DMA. I don't know whether this could be also set for the <img src="/ubbthreads/images/graemlins/beyond.gif" alt="" /> exe file, but if it could be done, we could be a step further. <img src="/ubbthreads/images/graemlins/winkwink.gif" alt="" />