Some more 'possibilities'...
- If you normally feed the books to the Nook with author as FN LN, and the Nook displays them as FN LN but in LN sequence, is it possible that the Nook is doing some sort of text manipulation to 'guess' what is the LN and what is the FN? If so, then mapping your author field to contain author FN LN [series (index)] may give the Nook a hard time figuring out LN and FN to create a sortkey for the book. It won't be expecting a text string that looks like the plugboard data. Is there a Nook book database you can examine to see what it has calculated?
- Perhaps the Nook has a similar problem to the Sony PRST1. I use a similar plugboard to map author on a T1, however, although the T1 puts the full text into its database in the author field and displays correctly, when it sorts it does not use the whole field as the sortkey, hence some books end up in the wrong sequence if you send a series piecemeal. With a T1 you can get round this by viewing books by Sony Collection, which are always resequenced correctly by Calibre every time you connect.
- Have you looked in Prefs - Plugins - Device Interface - relevant Nook - Customize to check that the settings are correct? Whatever they are try you could try changing them to see if it makes a difference.
- Have you tried using the Plugboard to map the Title field instead, i.e. prefix the Title field with the series info.
Sorry I can't help more. You really need another Nook owner to chip in.