Are you sure the second copy is not the old cover? It is expected to end up with an extra image in the front, since MOBI does not identify covers. The library metadata cover is prepended and identified as a cover, the old first image is just a page.
I cannot imagine how the book can still have the old cover if the image file is not physically present in the .azw3 (unless maybe it is referencing an image on the hard drive???

).