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There has been plenty of discussion on this in the past. And unless you change the book to epub3 and use the epub3 semantics, it is all a bit of guesswork as to what works. This is on both our and the softwares part.
The length isn't the issue. If the footnote is two long, only part will be displayed. And I'm pretty sure the renderer only considers the first paragraph as the footnote. I'd only expect to see it in the popup. And it doesn't look to long to be shown.
In this case, I think moving the destination id to the paragraph tag will work. Or wrapping the first line of text in the a tag. That's the first thing I would try. Or, depending on what the div is wrapping, moving the id to that might work as well.
The return links are not really needed as there will be a "Previous location" in the bottom bar after you go to the location. Most other ereaders and applications will have this as well. The two links might be confusing things.
The last thing I can think of is that the source link appears to be a number in it's own paragraph. To me, that would be a weird way to do a footnote. I could see the renderer deciding that this was a link, not a footnote reference. Especially if it is the first thing on the page.
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