I've noticed the same problem with pop-up footnotes. They only show the first paragraph, and they don't indicate whether there are more paragraphs. I'm not familiar enough with the CSS of Kindle books to know if there is anything you can do to fix this. If you can, you should make your book so that it doesn't use pop-up footnotes. The old style of going directly to the footnotes section was better, and it's the main reason I still read heavily footnoted books on my Kindle Touch.
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