Finally sorted it. Seems I have been flogging a dead horse. I suddenly remembered that some time ago I had corrupted a lot of my files as I was trying to improve my hard drive configuration, which involved moving my Data partition. It all went pear shaped and I corrupted a lot of stuff. I wondered if the books I had on my HDD and was trying to transfer to the Nook, were corrupt in some way, although they seemed OK. Turns out they must have been, and when I downloaded direct from the original CD to the Nook, it worked. I'm still not impressed with the way the Nook works, and organising the books into folders/authors seems very cumbersome, but at least I've cracked the main problem.
Many thanks to everyone for their help. Sorry I wasted your time.
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