PDF conversion is a minefield. Try using Mobipocket Creator. Free download at
http://www.mobipocket.com/en/downloa...ilscreator.asp. I've had luck with using that for more problematic PDFs. Results aren't always perfect, but I haven't yet found a PDF conversion process that always gets it right. Plus it leaves the HTML files in the book folder, making it easy to pop it into Sigil for additional cleanup, or further operations in calibre.