ADE must be reading the cover from somewhere else. It might be the last page in the book. The ePub standard supports adding semantics to files inside the book. So you can mark different sections as the cover, copyright, TOC and other parts. ADE might be using that to get the cover. But, I didn't think calibre did. If the book doesn't have DRM, you can use calibre to put the cover at the start of the book.
If you send the book to the device from calibre, you can set both the "send covers" and "always send cover" option in the driver. This will copy the cover that calibre has to the device when you do a send.
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