Hmm...
From content.opf of a sideloaded KePub that does NOT show the cover:
Code:
<item href="Images/cover.jpg" id="cover.jpg" media-type="image/jpeg" />
From content.opf of a sideloaded KePub that DOES show the cover:
Code:
<item href="Images/cover.jpg" id="cover.jpg" media-type="image/jpeg" />
So no difference there. And the href's are indeed referring to the correct location