you'll probably have to insulate the board edge with nail polish to keep the JAMMA video out of the switcher. i think the multiple signal paths are messing with the video for you.
before you go too crazy though, double check that straight VGA connection from the DB15 connector to your monitor results in a satisfactory display (eliminating the switcher). otherwise you'll be chasing a red herring.
12,13,14,N, and P are the pins you'll have to "paint" to insulate the video.