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try resetting all calibre convert preferences back to default for that book., then reconvert it. you may have left something in find & replace. ( leaving just one blank space in there can be disastrous)
you can post short extracts of text to show the problem if it persists.
+ check your workflow - i.e. that the book that looks fine on Kindle is the exact same file that looks wrong in calibre viewer , not a newer or older version?
+ confirm for us that you have latest version of calibre - I believe there was a temporary glitch to do with mobi font sizing in one recent version that was quickly fixed
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