From what I've tried it appears as the "move" command in vitashell is not working properly, I've tried moving the roms to another folder and they didn't show up, I then tried to copy and paste them and they appeared.
Try this, create a new foder inside data/, then find any of your roms that don't show up and COPY, then PASTE it into the new folder. Open up the related core (or any core and disable the filtering) and browse to your new folder, the roms should now show up. Or at least it does for me!