I have just installed the Game of the Year edition on to my new PC, and copied the saved games folder from my old pc, but the game won't recognise them.

The game on my original PC was the normal edition, with the expansions downloaded from Gog. Could this be why? Any ideas?

You could try to allow the game to generate some save files and then erase the save files and replace them with your own. The reason i say this is because my documents doesn't relate to a single directory but two or more locations. It is therefore possible to have two folders with the exact name in my documents while this is normally not allowed