ebr/Luke, I need help with this one. Recently I've had some similar problems with music library as other users where Emby was creating duplicate entries. I nailed that one down by turning off scrapers from Musicbrainz and AudioDB.  It seemed to have exorcised the duplicates. Then I had the problem where some song files and album folders were being populated with the wrong artist or album artist.  A combination of uninstalling scrapers and having to go back and rescrub all the metadata for all my