You might be looking at this in the wrong way.
If the code doesn't have p tags to indicate the paragraph, what does it have? Does it use two br's? Or something else? If it is br's, then adding the option "replace_br_with_p: true" into the personal.ini for the site might help. Otherwise, I suggest mentioning it in the FFDL thread might prompt a suggestion or a fix to the downloaded for the site.
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