It may be more of an Emplode 2.00-final problem working with 3.00-a3, but lots of times the uploads will just die after a few tracks and leave the database somewhat corrupted to the point where on next boot a rebuild is forced. At that point, there are a bunch of files that are in the DB, but the tunes aren't actually there because the upload got screwed-up. This happens on both my Mk2 and Mk2a over ethernet. I have not tried USB with 3.00-a3 yet.

I am using emplode 2.00-final because the one provided with 3.00 likes to crash before even loading the player database and I have no OGGs, so there is no need.