I don't think it is a bug. It probably works like side loaded content on the Nook, and is not seen by the B&N server.
I just downloaded the Nook for PC on a new computer and the "My Stuff" section of the library is no longer available. Is this a bug or has BN decided to have the reader be exclusive to books purchased on their site?
I use this section to load only the books I need on my PC and not my enitre BN library.
Try moving one of the epubs from a subdirectory directly to the root of MyStuff files (on android, it is NOOK\MyDocuments). Since the N4A 2.7 update, it cannot see subdirectories. If this is true on the PC version, try complaining loudly. This app should be able to transverse subdirectories.
Interesting, I'm running 22.214.171.12463 and it has "My Stuff." Do a 'Check for Upgrades' and install the latest version.