I'm guessing your black's look white and vice versa. Greens look red and blues look yellow or something like that.
This is because Nintendo boards output video in negative, while most boards (including JAMMA) output in positive, which "normal" RGB monitors expect. Nintendo used special monitors (usually the Sanyo 20EZ) that operate in negative.
But don't despair. A simple color inverter board (found at several sites, including Mike's Arcade) will allow your SMB to display properly on your monitor....