I got mine working. There were two potential problems with my setup, and I changed both at the same time, so I don't know which was causing my problem.
First, I changed my menu which required that I rename a file. I undid this change and went back to the original file name.
Second, my roms were saved in the sd2snes folder itself. I created a new folder on the sd card and moved my roms to that folder instead. My guess is that it was the second change that fixed the problem.