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Thanks for the clarification. I would have thought we would have made allowances for the NAV in the spine (otherwise there's no reason for it to be movable). I was basing my guesses off of the symptoms alone. But like you mentioned, I think there may be some confusion between the NAV and secondary html tocs going on here.
Perhaps the OP's epub doesn't include the NAV in the spine, and the secondary Toc that calibre may have created is what's appearing at the end of the book.
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