(Sigil creates .epub files, however, KindlePreviewer will compile them.)
I trust it's okay to hijack the thread, since the problem was resolved?
I write my Kindle books in html, and when I am happy with the result as uploaded to the KDP, I then open the html in Sigil and create an epub for Barnes & Noble. Because of the way I work--which I honed by hit&miss before the "mandatory" NCX file came into our lives--my Kindle books are innocent of this feature.
Would I perhaps do better to invoke Sigil from the start?
My interest is almost entirely with the Kindle, since Amazon routinely outsells B&N nine or ten to one; this has been my experience for four years now. Creating an epub for the Nook is just a courtesy to my friends who happen to own that device.