I have had some books where the Extra CSS doesn't work for the whole book conversion. For those books, I open the EPUB in Sigil and edit the various files as required. Sometimes it's as simple as editing the global style sheet. Sometimes I have to go into individual files. I have noticed that some books that have a class setting for the first few paragraphs of the chapter which has different formatting - such as side/top/bottom margins and line spacing etc - than the rest of the paragraphs in the chapter. Perhaps something like that may be the issue with the margin cuts? As the next step I would try opening the unconverted, original EPUB in an editor like Sigil (it's free and there is a whole section on MR related to this software).
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