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It's possible that you're seeing a difference in the renderer's used. As has been mentioned many times, KePub files use a different reader than normal ePub files; it's possible that what you're seeing is perfectly normal. Try other books and see if they're all the same.
The plugin doesn't do anything to the font size. It changes the ePub structure considerably, and it's certainly possible that poorly-written CSS in the book would not work with that, but if that's the case then that's a problem with the book.
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