Unpublishing not removing items

Under 6.5.2 unpublishing removes items that have been archived or expired from the publishing stream and the file system using FTP.

Under 6.6 unpublishing removes the items that have been archived or expired from the publishing stream but not the file system using FTP.

We performed a simple upgrade of an existing installation so the sites were created under 6.5.2

Is there any special option that must be set to restore the behavior such that Archive or Expired items are deleted from the file system using FTP?

The publishing logs indicate the items are unpublished as [ if ] Rhythmyx sent the commands to remove the items, but enabling FTP logging of client commands on the server reveals a command to remove the items was never sent. All subsequent publishing commands do arrive at the FTP server.

running [ rhythmyx-6.6.0-build-3206 ]

Thanks