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I also figured out that if I rename the epub as a zip file I can look at the actual files in it. I did so with the one where I renamed the files to lower-case and, yes, they were all actually in lower-case (and that's what the toc.ncx was looking for). I did the same for the earlier version (with the upper-case "Chapter-*" and those text files were, in fact, named with upper-case "C"s and, again, that's what the toc.ncx was looking for.
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