The timer is set to record on the tuner you are using. You can go to the tv activity screen and see if there is an open tuner.
Only one show was set to record and the Hopper's new UI apparently is too stupid to record on another tuner that's not being used. I understand that if all tuners are being used, it will ask to record but with only one tuner being used to watch and the two remaining tuners available, it should record without asking.
Would be nice if there was an option to tell the Hopper to record without notification.