This has been happening to me too. Even apparently with .lit files that were created from html.
Interestingly it's also happened when I converted a rtf file to lrf but somewhat randomly. I'm assuming calibre converts the rtf file to html and then to lrf. I converted one rtf file to 5 different lrf files which only differed in font size. In two of the files, the gap between the last and second last line of the paragraph appeared and in three of them it didn't.
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