When dragging your music to iTunes (or letting it read from a path) to build its initial library, did you let it look at any .m3u files? iTunes will duplicate the music in your DB if you do this, once for the actual track and once more for the reference from the .m3u file.

That's the only reason I can think of for duplicate entries in iTunes. Just delete all the m3u files (you don't need them for even semi-intelligent players), clear out all the music in iTunes and add it all back again.

Also, I always make sure to turn off the option which lets iTunes manage the location of my music. That way tracks are never copied by iTunes and instead are always added in by reference to their current location.