Can you provide folder/file names? I dont follow the naming schema 100% but Id use Ferry Boat Fred {tvdb-394549}/Ferry Boat Fred - S01E01 - <title>.<ext> format myself. Along with the server logs ? mgiht also try doing the plex dance. As a side note I do not use the automatic scan feature If plex tries to scan the files as they are still being copied into their location plex may see an incomplete file and just ignore them.
