Thanks, I'm having a look at Beyond compare. It has a 30 day trial which is useful.
I also found
http://www.fastsum.com/ which has a useful utility for this sort of thing. It will go through whole trees and produce MD5 values for individual files / folders - storing them in the folder. Then you can just run the utility and it will calculate and compare the MD5 for the current file and last MD5 calculation.
This is idea for future copying (since the MD5 values will be copied too) but not that easy at the mo to use.
Anyone got any idea how to copy all *.md5 files recursively from one tree to an identical tree on another disc ??