I started from scratch, deleted the folder from external hard drive and repeated all the steps again to copy it. Possibly I had only selcted itunes music folder rather than the main complete itunes folder. Anyway everything has now copied over, playlists, ratings, podcast etc etc, no missing tunes all running fine.
I just hope that doing it all twice won't cause ny problems later on as now I have the original itunes folder that was incomplete in my trash and the new itunes folder in the music folder (there wasn't a long wait whilst it linked). I will find out when I empty the trash I guess.