if the playlist itself is only half populated then i would say the files failed to copy. I am surprised that MB would not have reported any error though.
I suggest you check the error log (help/support/view error log).
if there are a bunch of errors, maybe you could paste one of them here. In all likelyhood it will be a random device error and trying again might work.
I am not willing to spend much time on this though as i dont have the time to spend trying to solve the quirks of every device out there.