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Well, PDF is a non-reflowable format, and ePub is a reflowable one, so of course you can expect to have drastic differences in the "page" layout you see on your device depending on things like margins, font size and the like. From what I know, Calibre tries hard to preserve other formatting (font attributes and the like). An example or a more precise explanation of what you're seeing vs. what you'd like to see would perhaps help.
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