I know kindlegen can be very fussy about top AND bottom margins being simultaneously applied through CSS to <p> and other block tags. One or the other seems to get ignored at times. Especially if the margins are specified in em's. I've had better luck designing layouts where you can get the spacing you want with top-margins only. Or using pt's instead of em's.
Another trick is to run the epub through calibre's mobi conversion process. If the results look the way you want them to (on a Kindle or in Kindle previewer)... use MobiUnpack to see what's going on. Or even just feed the results of MobiUnpack (the opf file) to kindlegen.
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