@davidfor,
I can confirm what jiembe says. A source epub which has a ToC entry in the NCX for each file including the cover page (a standard calibre SVG-type cover page) produces a kepub which still has the cover page but the NCX entry for the cover page disappears during the conversion process.
An epub-to-epub conversion using the same source epub and conversion settings does not lose the cover page entry in the NCX.
I can post a small test epub if you need one.
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