I don't know the answer to the problem you're having, but I'm sure someone will be along who does.
What I do when converting from PDF is export to HTML and open the HTML in Sigil. In Sigil I get my chapter headings and breaks and any other formatting how I want it and save it as an ePub. I then convert the ePub to Mobi for the Kindle. This gives me the best possible looking book and it's easy to do additional editing in Sigil and re-convert if needed. It also gives me the little chapter marks in the progress bar on the Kindle, which is kind of nice.
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