Maybe it can't enumerate the files because they're not patched with SuperMDPlug host or you didn't inserted the sd cart correctly( ? ) .
I'm working on a batch-patching app that will co operate just like md myth and the plugin.
No, that can't be it. It will show ALL files regardless of whether or not it recognizes them. The only thing no entries could be is a problem with the card. Not all cards work - I made a list of working cards I have in the v1.0beta thread. I should probably split it off by itself.
Try a few different cards and see what you get. If none of the cards work, then something else is the problem (unless they're all the same brand and model card, of course). If you find some work and some don't, report all that so it can go in the list.
Also just a quick check, but roms work when flashed to the Neo2-SD, right? They show in a list on the first screen of the menu? The top line of the menu says Neo Super 32X/MD/SMS Menu v1.1b3 (or b2)?