Calibre doesn't know about an sqlite database for the nook, and puts nothing in it. That would make an excellent project for someone. I would consider it, but I don't have a nook, and couldn't buy one here if I wanted one.
In the meantime (and it may be a long meantime), to get any metadata, the nook must be parsing file names. I suggest you look at the names that work and don't work to see if you can detect a consistent difference. Then, if possible, adjust the save template so that the 'correct' string is always generated. As a random guess, I would suspect that if series information is included in the file name, the nook wouldn't know what to do with it.