The title says it all. Some programs (I have not established any pattern) that have been watched and deleted persist on the DVR Recordings tab. Many times programs that have been combined to a single icon with multiple programs as indicated by the "(n)" to the right of the icon, contain programs that have been watched and deleted when a single instance is correct. These do not show up on the main Hopper.
P.S. This has been happening for a long time and not just with the recent update that has caused the remote control numeric keypad to stop working with subchannels.