When I run SongKong on a folder full of songs it will rename some of the songs and move them into new folders but most of them are left in the original folder unnamed even though SK fingerprints and saves them to itunes. I get no error messages, am I doing something wrong?
Fingerprinting means that an acoustid has been created for the songs, most songs can be fingerprinted but having a fingerprint doesn't guarantee the song can be identified there may be no link from the acoustid to a song in the MusicBrainz song database. The acoustid is saved to the file so it doesn't have to be recreated so when you first run your songs against SongKong most files are updated even if your songs are not actually matched.
Files are only moved if they are are actually matched to songs on a release, take a look at the report that is created that should makes things clearer. Note by default SongKong is quite strict in that even if an individual song can be matched to a song but all the songs within the folder containing it cannot be matched to an album then it is treated as not matched. If you want to loosen this criteria you can disable Only allow match if all songs in folder match to album however you shouldnt do this if your songs are already nicely organized one folder per album.