This seems to be a common issue after a rebuild/restore. Any shows recorded in the interim are left in an orphaned state. I found many threads about this occurrence so it's not unusual. It seems like the only way to fix it is for an administrator to go find those shows and move them to your Imports folder.
This seems like it should be an automated task that happens once per day. The server should look for files that don't match the database and pull them back in to the fold. Don't make us do this manually!