When editing or adding to a playlist in the root directory, I noticed the Artist, Source and Year fields for that playlist had all been set to "Various" rather than left blank. Any contents from that folder/playlist were then dumped from that folder into the root on the next sync because their ref counts had all be set to 0 during the sync.
Also, creating New Playlists do not work either....
FInally, I was able to copy tracks from one empeg to another, but I could not click on an entire playlist and copy that from empeg0 to empeg1.
I used Jemplode 61 mainly for updating HiJack via ethernet, so I'm not sure if 64 is the cause.