@Marco > I suspect if you were to check the filenames / paths of those duplicates you might see why they're being duplicated when imported -- rekordbox sees it as a unique song, a new addition.
Do you have this checkbox ticked: 
If you do, any changes to the title, artist, or album, will result in iTunes moving the file to a new location.
The other reason this might happen is if you use Windows and your music is mounted externally - the drive letter may be different from one to the next. If you use a Mac, and mounted two drives with identical names, it would name the second drive with a "1" at the end, thus creating a different path to the files.