I had a similar issue with my Playstation 2 hooked into my Denon AV3801 via S-video. It was very odd...when certain types of screens (load screens and the pause screen on Madden 2003), I would lose the aspect setting, the color, or sometimes even the complete picture. Turned out my S-video cable was bad...I figured it out when one time I lost the picture, I just randomly decided to play around with the connector. I replaced it with a new cable, and all was fine.
May or may not be the same issue you are having, but the symptoms sound similar...