Which circuit did you use for S-Video? I recently installed S-Video into a JVC X'EYE initially using this design:
http://www.jamma-nation-x.com/jammax/genesismods.html
It looked great on my personal Sony Trinitron but once the owner got it back he found the colors would fluctuate between too bright and too dark IIRC; thing is he too used a Sony Trinitron but a different model. I replaced it with this design:
http://gamesx.com/wiki/doku.php?id=a..._1_s-video_mod
Bit more complicated but looks just as good. He found it to work perfectly with his Trinitron as well as several others I tested it on. Not exactly sure why the simpler circuit didn't work across the board.