Thanks for the reply! I found out what it was, when I tried to do the 8 boot reset. I still had Clockwork Mod installed on the main memory, and that stuffs up your recovery options.
So I reflashed the image on the Nook, installed the 1.3 update, and redid the card. It works a treat. And just to show that it wasn't a fluke, did it with my friend's rooted Nook Color, too.
Clockwork Mod must do a lot of stuff to the internal memory, and I hadn't realised that it hadn't been uninstalled when I did the original restore to stock.