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I have done some testing, and the problem @Semwise is seeing is triggered by having entries in the NCX that point to anchors. If there are no references to anchors, everything works fine. Where there is a reference, when you use the navigation bar to jump between chapters, if you reach a ToC entry that points to anchor, it gets stuck there.
The attached test book demonstrates this. This has some chapters with anchors, and some without. The chapter names indicate which type it is. If you start at the beginning, open the navigation bar and tap the right double arrow a few times, it gets to "Chapter 3 - With anchor" and gets stuck. You have to page out of the chapter for the right double arrow to work again. Then it stops on "Chapter 4 - With anchor". Page through some more, and it gets at "Chapter 6.1 - With anchor". And then "Chapter 9 - With anchor".
Within Chapter 4 and Chapter 6, the behaviour is worse as there are multiple ToC entries in each of these files. But, this is what happens in 4.12.12111.
So, there is a change in behaviour with 4.13.12638. It affects a particular style of building the ToC. I haven't seen it as I strip out unnecessary anchors if I see them. But, a lot of my books don't have them at all.
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