Hi,
I wrote a new app for nookColor that fixes some of the cover issues.
If you have cover inside the epub or a cover image file with same name as the book ( the way calibre copies), it will update the database with the correct cover and covers will show up in B&N library and home screen. This should work for pdf & doc files as well.
You can also add sideloaded books to B&N home screen.
App is still beta version and I still have lots of testing to do before B&N opens their app store. But you can give it a try and give feedback.
http://nookdevs.com/NookColorFileManager
Thanks