I just noticed that "tools_v2.3" & "tools_v2.2" has an .pwy file called "ePub_Fixer.pyw". In reading the readme file I see it says "ePubs are specially crafted zip archives. Unfortunately, many of te DRM encoded Adobe Adept and Barnes & Noble ePubs are not "proper" zip archives in that the names of some files in the zip central directory do NOT match the local name given in archive itself. This type of zip archive is technically incorrect/corrupted and can not be read by many other programs."
I wonder if this would fix the cover problem. I would check but my NC is headed back to B&N with a new replacement coming. Unless someone else reports on it first, I'll check when I get my new NC.