Not sure what the glitch is either but if they physics calculations are tied to the frame rate then a different monitor refresh rate could cut the speed of the game down greatly. I'm not sure how things are set up in the code, but each frame should be calculating the changes in speed based on the time that passed from the last frame.
I see. The entire engine is set to run at 60 frames, so I'd have an insane amount of work to adjust every single event in game, in every stage, to work with a delta in time from the previous game loop.
Can you try to make a link to the exe of the game, open the link properties and add the command /MIS1 in the destination field after the double quotes of the game path? The command will tell the game to run in "machine independant speed" mode, and maybe that can solve your problem.
It should look something like this:
"C:\BLAH BLAH BLAH\Sonic3D2d 1.02.exe" /MIS1