Yes, from testing the Neobitz in a D-lite supergun I remember hardly any, if any, JAMMA games worked with S-Video, but they all worked with component. I tested well over 100 PCBs... maybe upwards of 200 as time went on.
I hope this doesn't mean gloom and doom for your setup (if you won't have component). Have you S-video experiences been any different than mine?
By the way, you should let your TV rest for 30-40 minutes before you put it turn it on its side. Then you won't get the crazy colors. The sooner you turn it on its side after recently being turned on/off the worse your color issues will be.