I know this is an ancient thread, but it seems relevant to my issue.
I have a vs. unisystem setup and P1/P2 controls are reversed for vs. Dr. Mario. P1 joystick/buttons control the P2 side of the screen and vice versa for P2. I pulled the roms and installed SMB and the controls are fine... P1 controls mario and P2 controls Luigi.
Any ideas?
-Brian