Sometimes when it looks like there are only the markers for major sections (e.g. Part 1, Part 2, etc.), the book actually does contain more for the individual chapters as well. But they're invisible due to the way that Kindlegen (and presumably Amazon's DTP) handles nested NavPoints in the NCX file.
However, you can navigate between them by going to the start of, say, Chapter 1, and then flick the 5-way controller to skip to the next. I wish the Kindle would show them all in the location bar, even if they used a different style of "dot" to indicate some were a 2nd/3rd level navpoint.
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