My guess: you have one or more of the options ‘Process Playlists’, ‘Process iTunes files’, ‘Process .m3u files’ enabled.
I think the easiest way to fix it is this way:
Visit the webadmin page. (http://:3689)
Go to Configuration. Click Show advanced config.
Disable any or all of the above options. Make sure you hit save.
Then, to get rid of all the playlists, I think the easiest way is to delete the database and let firefly create a new one:
Shutdown firefly. Delete the database. (songs.db or songs3.db)
If this doesn’t fix your situation, I probably misunderstood yours.