This is exactly my issue with the game. I'm on an ASUS W3V laptop here and it has a Mobility Radeon X600 graphics card. I can't see how this issue can't be fixed.
I also have a severe issue when I try to beat the game... The video decides to play at 1 FPS and the Sonic CD process eats up all of the CPU at a super high priority and thus takes a long long time to open up task manager to close it. Otherwise, the port is pretty nice for me.
I have this same issue. However it doesn't bother me because I know my graphics card sucks ass. I kind of expected things to not be at their best on my pc. How I get through the intro and ending is to constantly press enter until it finally registers it (which usually takes just a few seconds).
One unrelated thing I found might possibly be an oversight. When in Time Attack mode, water does not effect time at all in the Special Stages. It might be intentional, but I don't see why it would be. That is, unless the original game did the same thing.