I realise this is years late but I just had the same issue as the OP and it was driving me mad and as I found the solution to the issue in my case, I thought I'd share it. I'd tried a FAT32 formatted SD card and a WFBS one. I'd tried various versions of the game files and ripping directly off a Wii disc and a couple of games wouldn't show up whislt others were fine. I tried categories, games types, parent controls etc. etc.
It turned out to be the star icon in the top left of the USB Loader, which I assume is favourites. When I clicked it, all the games showed up! That's 2 hours of my life I'm not getting back but hopefully this info may save someone else wasting time.