I've just found an answer that worked for me in the FaceBook Nook Discussion forum. Here it is for anyone else that might have the same problem:
"When I sideload content from places like sony, smashwords, etc, I have to manually import it into ADE. (these are all epub files.) first I download the books to my computer, into a file folder I've created for ebooks. then go to the dropdown "library" menu and choose "add item to library". open that ebook folder, select the new books, and you should be good to go.
This usually works for me when a book does not automatically open in adobe, like books from the public library do."