This is fixed in 2.1.0.4. In the meantime, if you encounter this it is probably caused by you having "move on complete" set and have unchecked "only if in default dir" in config->files.
To resolve the problem:
  1. temporarily deselect "move on complete"
  2. save config settings
  3. remove the swt/core torrent you have just downloaded from azureus
  4. restart azureus
  5. redo the update
Thanks!