Is your VGA adapter something like this one?
http://www.amazon.ca/gp/product/B00DJ16 ... ge_o01_s00I got this one and I have the same problem you do with SNES (S-Video or composite), Genesis (composite), and Sega Master System (composite).
I also tried the NES through composite and had a different problem - the colours were slightly off, within range of the VGA converters HUE controls to correct, but I don't have to adjust for the consoles that work properly.
N64 (S-Video), Gamecube (S-Video), Saturn (composite), and Amiga CD32 (S-Video) all work fine.
There must be something different with the video signals the SNES, Genesis, and Master System are outputting that the VGA Converter doesn't like. I thought this might be a problem of low resolution until I tested the NES, perhaps there something wonky with the refresh rate?
I'm waiting for some new dedicated S-Video cables to try out with the SNES. The only one I have to test with now is a crappy 3-in-1 Gamecube/Xbox/PS2 cable that makes the screen door effect. I'll let you know if the new cables change anything.
I bought this thing mainly for S-Video consoles because my TV doesn't have an S-Video input, I really hope I find a way to get SNES working.
