Originally Posted by AnemicOak
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.
I actually tried what you suggested and downloaded Sigil and then saved an HTML file using that program. I converted in Calibre and I still get the same problem where the text will not flow to the very bottom of the screen. So Im' really not too sure what is causing the problem. Do you think it might be something wrong in the HTML file itself causing the major break in lines?