The question is, are you doing the Plex Dance between every one of our suggestions, and have you completely removed those files from plex, and not just copied them somewhere else for testing? Plex attempts to detect file renames and preserve association of previous metadata and view history.
If you are using the proper Plex naming schema, and have performed the Plex Dance, the only other reason the files wouldnt show up is if the files where corrupt or not valid video files.
