I believe you will find that at this point, the transfer of a book from the Calibre server to the Touch is purely that of transferring the ePub file AS IS. Try adding the ePub in question to ADE and see what IT shows as a cover.
Note you have to explicitly do a LIBRARY | ADD ITEM TO LIBRARY in ADE; just opening an ePub will NOT add it to the ADE bookshelves.
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