Many of us are convinced our computers have minds of their own. In this bizarre case of iTunes moving music files around, there may well be a ghost in the machine:
Ok. I got one for you that has stumped EVERYONE that I have proposed this problem to, including Mac Geniuses and numerous techie friends.
iTunes keeps all music organized inside the Music folder in the Home folder. For the last several months, periodically when I add a new song, or change something regarding songs already in the library (add artwork, adjust genre, etc) SOME songs will relocate themselves to Macintosh HD >Music >iTunes >iTunes Music [outside the Home folder].