Hmm, well, as far as games not showing up, make sure you don't have any favorites or categories set. That might help. I know you said you got the names right but, just to be sure, I always just use Wii Backup Manager to "transfer" the game to the drive. That way I know it's in the right format, place, name, etc.
As far as games not working, did you do an update recently or something. You could always re-mod with ModMii just in case. You could also try temporarily moving settings files so it makes new ones in case they're what's breaking stuff. Doing a chkdsk on your drives and then defragging them might be a good idea in case it's because the drive or games got corrupted or something.