Sync iPod from QNAP NAS

Win7 laptop with iTunes updated.

iPod touch connected to laptop.

QNAP 439 Pro NAS on network with all the music files in one folder (called Music), with subfolders for each artist and album.

I have the default Library location setup in preferences in iTunes.

I added the NAS folder to the Library using the File/Add Folder to Library menu command.

When I try to sync the iPod to get the entire music library onto the iPod, some songs are missing.

It will load parts of albums - even ones bought on iTunes, but will leave out random songs from the same album.

It pops up the error message saying "some songs were not added because they could not be found", and then lists about 100 errors in the bottom of the window.

There is plenty of empty space on the iPod to contain all the files.

I even tried to "force" it to add the missing files using the AutoFill function. Did not work. In fact, it added duplicates of some of the songs (uggh).

So...two problems:

Missing files during sync.

Duplicate files on iPod now.