The .ncx file is the table of contents for your book. Two working entries presumably means two entries where the links actually work (ie; chapter 1 with a link to chapter 1, chapter 2 with a link to chapter 2). Sorry, but I'm not familiar enough with the workings of Scrivener though I would think it would have an easy method of producing a valid toc.ncx with at least 2 entries.
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