I don't believe it has anything at all to do with your nook. It's an ADE issue. I think there are ways to fix it, but I don't recall. I have the same issue with my ipad. In fact, sometimes the cover isn't even displayed within Adobe.
The books with generic covers are probably DRMed ePUBs not from B&N.
I purchase many non-agency ePUB titles from sellers other than B&N. All ePUB files, DRMed or not, can be sideloaded and read just fine on my NOOKs. But DRMed ePUBs not from B&N (such as those from Kobo), display with generic grey covers. I do not think there is a work around for this.
If I am wrong or if someone else has discovered one, please let me know, too.
PS: If a PURCHASED non-DRMed ePUB displays a generic grey cover, you CAN add or generate a color cover via Calibre and reload the title with its new cover art. (ADE is the only option for library books, isn't it?)