Well, I found one (fairly unsatisfying) way around this issue. I created a new user account on my computer and ran the Nook for PC program from their without a hitch. The magazine I recently purchased worked wonderfully in the new user account, so I the folder it was in (the folder was in My Documents > My Barnes & Noble eBooks > e-mail_address) over to my original account and placed it in the same location (only this time in the original user's account -- Computer > Disk Drive > Users > Original Username > My Documents). I then opened Nook for PC in the original user account and drug the .epub file (located in the folder named after your e-mail address -- My Documents > My Barnes & Noble eBooks > e-mail_address) into the program. The magazine worked! Once this was completed, I went back into the library (still logged into the original account and without transferring anymore files) and all of the content seems to be working properly. I suppose the program just needed to find the actual library on the computer again.
Anyways, so things seem to be working well now. It is a bit of a process, but I hope this helps someone in the future!