I'm not sure. I have a couple things to try though. Keep in mind that I have a Kindle Fire HD, not a paperwhite. When you convert them, put them in either AZW3 or old MOBI format. I have had trouble with margins being messed up on a very few MOBI files, but once I made them AZW3, that worked out well. I'm no expert, but give it a try.
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