I'm not sure about the other sonic games, but sonic 3 and sonic and knuckles have heavy flickering in the 3d bonus stages where you get chaos emeralds. Does anyone else have this problem?
I already have xfb set to virtual. Also, only the 3d bonus stages are flickery not the entire game.
Long shot solution: See if D3D or OGL works better. Also, see if previous revisions do any better.
Turn up the emulated CPU clockrate to 200%