Strange.... <img src="/ubbthreads/images/graemlins/think.gif" alt="" /> Maybe something in your system doesn't like the roof fade in/out effect. Have you checked for updated graphics drivers? Is your desktop set to 16 bit colour depth?

In the configuration program, have you tried checking Alphabit or unchecking Smoothness? Switching to software or DirectDraw?
In the game, have you tried reducing the visual quality or disabling ztunnel? I temporarily turned down the quality to see if it would effect performance, but didn't notice a difference (1024x768, high quality, gamma correction 1.35, hardware acceleration on, but on a desktop system with windows 98).
Can you try reducing the resolution, at least long enough to see if that helps or not?