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The order of the TOC.NCX didn't match the order of the spine. I've verified this with other books with more blantantly obvious examples. The TOC.html doesn't matter it seems.
One being a book which decided to link a chapter that was in the back of the book, long before it totally out of order (the TOC.NCX was created based on the source document)
On top of that, I think Calibre just ignores this error and makes the MOBI anyway. But when you submit that mobi to KDP, KDP does not accept it.
It would appear if you want a proper mobi to be submitted to amazon, the spine needs to be in order with the TOC.
I honestly didn't know this was a thing until now. It answers a lot of "why this mobi won't be accepted" questions. The TOC.NCX isn't used in Kindle devices that are common, but it IS used in some of the apps for other devices.
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