True... The only thing I can think of is that a connector pin (or whatever you call it) on the back of your s-vid cable (that goes to your multi-out port on the SNES/N64) is mis-aligned somehow that the SNES isn't reading it right, but the N64's fine with it. I'd suggest getting the cable from a place that you can return it for a refund. Just in case the new cable has the same problem.
Btw, for the SNES's are the top and bottom gray plastics different in color. I know that the old units used cheap plastics that discolored... if both units are like that then maybe they're of the same batch, therefore the problems exist in all of the same model types... or maybe I don't know what I'm talking about and am pulling stuff from my ass.
All are guesses, since I'm not a pro at this kind of stuff... But I'd go with the idea of buying another one from a place w/ a return policy.
Enree.