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The "linear='no'" was the surely culprit. I don't think Sigil has the facilities to alter/remove/add the "linear" attribute of spine items. So it (Sigil) probably just left that entire entry alone. That's why you had to change it manually in the OPF.
But the renderer in your reader is ultimately responsible for how "linear=no" gets interpreted. It looks like in your case, it didn't remove it entirely from the flow of the book, but did leave it until very last.
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