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Given both 0.9.16 and 0.9.991 and calibre all are saying the same thing, your opf is broken and does not identify the ncx appropriately. Note the ncx id should also be included on the spine attribute.
Please pm me a link with a list of all of the files in the epub (run the equivalent of an unzip -t on it) and a copy of both the ncx and the opf file (*before*) they are loaded into Sigil.
And I will verify if there is an issue.
There are many causes for graphical glitches and so I would not worry about the alpha at all.
KevinH
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