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OK... thanks for the info, twedigteam. I created a small test file, but can't reproduce what you're experiencing, so hard to know what might be going on I'm afraid.
However, that facility in Kindle Previewer to view the NCX content is purely for the purpose of checking that it is an accurate map of the ebook content - it's not a feature on the Kindle itself. Unlike EPUB viewers, the Kindle doesn't use the NCX file to display a TOC - the only TOC you can display to the user on a Kindle is an inline HTML TOC. So this shouldn't be an issue with the published ebook - just a (currently) unexplained quirk in Kindle Previewer.
I've attached a copy of the test MOBI file I used to see if I could replicate what you're seeing, so you can use it to compare with the file you're currently working on, if you want. Also attached the EPUB file I used to generate the MOBI file.
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