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I decided to use the restore feature of the plug-in. That put the books back in their original collections after a reboot. I then ran the create collections as before. The only thing I did different was to use Calibre to eject the kindle, which I don't think I did before. I then restarted and this time the books are in their collections and the one new collection created via the custom column has the one book that belongs, in it.
It worked. Either the eject via calibre is absolutely required or... I don't know what made the difference.
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