Sorry I may have misled you with my initial post. Everything was transferred fine and I have been using my new WD HD for a few weeks now.
The files have vanished after being saved on the new HD. They never existed on the old one (that would have been the saving grace if they were).
I see from other forums this seems to be an issue with WD drives.
I just wanted to share, incase somebody experienced the same and managed to get their files back.