I can't reproduce the problem with covers on my Voyage - I see the correct covers in grid mode.
Looking at my QuickLook cover software, I may have a clue for you.
It has two algorithms for finding the cover. The first is to select the first picture in the file. I suspect that may be what the Kindle cover hack is doing.
But to find the correct cover, if the book has an EXTH header you need to find record 201 in the EXTH header, which contains the picture index for the cover image.
This might be covered in the MObileread wiki.
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