I just want to close out this thread to say that when my book published in Amazon, I went and bought the Kindle version. This means I got it delivered as a "book" instead of a "document" as I had been previewing it.
It was very different. Hyphenation works correctly now, as do the pop-up footnotes.
So the lesson learned, as others have pointed out above, is that you can't really preview your book in the exact way people are going to experience it when they buy it from Amazon. There's some "magic voodoo" that happens to your book when Amazon sells it in their store.
Thanks to everyone who contributed here.
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