It's entirely possible there is a glitch where the UID for the database is off and thus loading the wrong physical file when the song is loaded. My recommendation would be to test with a blank database. You can do that by following these steps:
1) Close rekordbox.
2) Find your rekordbox database...
Win 7/8/10: C:\Users\yourusername\AppData\Roaming\Pioneer\rekordbox
3) Rename datafile.edb to datafile.edb.old
4) Rename the datafile.backup.edb files to .old as well.
5) Launch rekordbox and import one of the tracks you knew to be problematic.