[GeoffR]

That NCX should be fine for an epub as everything in the NCX toc appears in the same order it is in the OPF spine, but for a kepub it has two problems:

1. Some files in the OPF spine are missing from the NCX toc: e.g. titlepage.xhtml.

2. Some files appear more then once in the NCX toc: e.g. sher_9780465022342_oeb_c01_r1.html.

Edit: I think the first is the main problem, that is what will be affecting the page numbering. The second probably just affects the chapter graph, as long as all the references #h1, #h2, etc. are in the correct order within the html files themselves. But I might have that backwards.