Although they are not named through the database, I have my own naming system, before they would always be picked up. Usually, the metadata would still be found, but if not, I would use my file name for the game and the rest of the metadata would be blank. I could then either search for a metadata match or input my own, but the game would still run regardless. Even the games in my .m3u folders have my naming convention and are still being recognized to import. Those are the only files though. For example, 200 PS2 games (my naming convention), four of which are multi-disc. Launchbox will find and want to import those four titles, while not even seeing the other 196.
[EDIT] I still have no idea what the problem is, but I decided to move a few into the designated folder rather than having it redirected. That fixed it for now, but that still limits me to a small hard drive. I consider this closed, until later.
Lahrs's post in Not finding all, barely any, games was marked as the answer