I have managed to solve the problem myself now. I re-uploaded the borders, derived, fpclass,overlay,private,themes,vti_cnf and vti_pvt files in the hope that it would be one of them, and hey presto! it worked. Which one worked I am not sure, and quite frankly and not over bothered, as long as it worked.
If anyone has any ideas which one it was, I would like to know, just out of interest, but the fact that it has worked is enough for now.