When I was purchasing a SNES->USB adapter, many of them stated that they did not work with non-standard controllers. There may have been one that did, but I forget.

Mine doesn't say what brand it is, but it's the gray box with a purple bar on it. I think it was the most compatible one. $30 on eBay.

You may try posting on the EMU forums. emutalk, ngemu, emuxhaven. Good luck.