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Short answer: No.
Long answer: pdf is a terrible format for conversion. Calibre uses pdftohtml internally to convert a text based pdf into an html document. From there it is converted into whatever format you want. This as with almost all pdf conversion issues in Calibre is due to the limitations of pdftohtml and the complexity of pulling text out of a pdf file. The only way to solve this issue is for someone to come up with something that works better than pdftohtml (this isn't nearly as easy as it sounds, I've tried and pdftohtml still produces better results).
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