(don't forget to check the hidden folder 'recycled' if you are on windows)
I'm on Linux, so that directory cannot be the cause of the problem. I did check the root directory for hidden folders though, I found nothing interesting.

I also checked the properties of the duplicated database entries. Both were stored in the directory
/Music/Black Lab with filename
Mine Again.mp3.
[Update] Reinitializing the database worked.