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Ok, looking at that image, you will probably find that each of the "paragraphs" on your image were probably individual lines of text on the pdf. At the end of each line on the pdf there would have been a [CR] (Carriage Return) which would be interpreted in HTML as "New Paragraph". This is probably why you are seeing what you are seeing. What is needed is to strip these out when the pdf is being converted. How you do this in something like Calibre I don't know, but there is probably a setting.
I know this is not a solution to your problem but hopefully somebody can come up with something for you.
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