Are any of these soup playlists or just regular ones?
All regular

What OS are you on?
Linux (RedHat 7.2)
I tried to create a similar situation on mine and I can't it to happen (on Win2k)...
I can't make it happen consistently either. In fact, after changing those playlists by making one cut/paste at a time and syncing in between I haven't gotten it to happen again yet since.

Do you cut with Right-Click=>Cut or Ctrl-X?

Right-click.
Do you select from the tree or from the table? Same for paste -- do you right-click=>Paste into the tree or the table?

I was doing it all in the tree.

Also -- how are you launching jemplode? Are you just replacing the jemplode20.jar in your install dir and running the exe or do you have your own JDK and you're doubleclicking jemploe20.jar?

I replaced the jar and run the executable.

I'm trying some things to see if I can get it down to something that seems reproducible, and so far, losing.