In calibre, it seems some books that show a basic cover, do not have it set properly - after changin the cover in Calibre, if you try to take the cover image from the format, it is corrupted - I've seen this on a couple from PG.
Turning cover image semantics off and back on in Sigil, generally makes the cover setting take.
Might try that other option, if it can fix the iffy ones in a single step.
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