Sorry, but I am having trouble working out exactly what it broken.
First, could you give a small example of what is going wrong? I have tried to decipher your photos etc but am not sure I see it. What I think you are saying is that the Nook is displaying something different from the filenames produced by save-to-disk, and that the filenames are correct.
Second, you mention plugboards but show filenames. Plugboards do not affect filenames in save-to-disk or send-to-device. They affect metadata inside the book. So:
1) What is the template used for file names in save-to-disk?
2) What is the template used for file names in send-to-device?
3) What plugboards have you defined?
I think that the Nook gets its information from the metadata inside the book, e.g. the info set by a plugboard. My guess is that some template in a plugboard differs from the save-to-disk file name template that is working. Also, if the nook gets metadata from the book then you might need to delete the books from the nook before resending them. I don't know what causes the nook to re-read the metadata from the book.