I ran into the same issue and finally I put all songs into [Memory Card]\My Files\Music folder (not in the sub-folders any more). Music player then is able to display all the songs. However this left a huge list of songs. To organize these songs, I created a bunch of 'playlists' and assigned songs to the playlists.
Another issue is that there is no document to show how to remove/delete undesirable playlists. So now I have a few junk playlists hanging around.
This music player is too primitive. B&N should provide a desktop software, like iTune to iPod & iPad, to manage the libraries.
To delete a PlayList you go to the screen that shows all your playlists. Then "touch and hold" on the playlist and a menu will popup that will let you delete or rename it.
Did you check to make sure you didn't copy the files to the music file on the NT itself? The first time I tried to copy a movie to my wife's NC, I didn't realize that when I connected the NC to my PC two windows opened one behind the other showing the NC drive and the SD card drive (I could only see one of them). I accidentally copied to the wrong drive, but realized when I could not find the movie on the SD card and found it in my files on the NC. Just a thought.
For debugging purposes I would start all over again:
1. Removing all the folders
2. Verify that all songs go away in the music library.
3. Add half a dozen folders see if they show up again.
4. Verify they show up in the music library.
5. Add yet another dozen folders.
6. Verify they show up again.
If everything above works then you can probably figure that there is a directory (or file) name that is making the Nook spew. (Maybe it doesn't like spaces in directory names? Or a foreign character?)
Then you could maybe copy about 100 folders at a time and verify they show up each time and keep going until done or until failure. (Upon failure you can take further steps to narrow down which folder or file is the problem.)
I took your advice. I deleted all the songs. Then copied them over in batches of about 100-200 at a time. Amazingly, they all show up in Music Player now. I thought you might be right about a bad character in the filename because I had a similar problem with the NT reading PDF files with a '#' in the filename. But since all the same files are now on the NT SD card and Music Player has them all in the list, I am not sure that was the problem. Possibly more likely to have been an issue with adding too many songs at one time. Who knows?
I had the problem that my Nook Tablet showed only the music loaded into the Nook music folder, and not the music loaded on my SD card. I discovered when looking through what was on the SD card that there are two music folders. One of them is in the top level of folders. The other is a subfolder in the "My Files" folder. The music on my SD card was stored in the top level "music" folder.
When I plugged the Nook Tablet into my laptop, I was easily able to move the music on the SD card from the top level "music" folder to the other music folder. So... to find it in the library I would have to look at the SD card, choose "My Files" and the subfolder "Music."
When I disconnected my Nook from the laptop, I opened up the music player and it now showed all my music.
I had the same issue and what resolved it was this.
With your NOOK Tablet on, open Music Player.
Now quit Music Player and turn off the Tablet.
Pull the SD card and Reboot the NT.
Open Music Player (it will be slow to open).
Quit Music Player and turn NT off.
Insert SD card and Reboot the NT.
Open Music Player.