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It would probably be better in the calibre forum. But quickly: the problem is that the ebook in question was built with no ncx file... that's what generates the chapter markers. You may be able to fix it with calibre, but that depends on whether there is an easy way to tell calibre how to identify (accurately and consistently) where a new chapter/section starts (completely independent of the inline Table of Contents).
You could also convert it to epub and open it with Sigil to generate your own ncx and then convert it back to mobi for the Kindle.
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