The receiver will only deliver 1080p when it is tuned to an On Demand program in 1080p, or when you are doing the test. Otherwise it will deliver the resolutions you checkmark in the menu. If you set native off and just checkmark 1080i/p, all signals from the receiver will be 1080. If you set native on and checkmark all the resolutions, the receiver will deliver the original resolution (480/720/1080)
The DVR could have accidentally put in SD mode. Hold the EXIT key and see if it will give a message about whether it is HD or SD mode.
If you have a VCR or DVD recorder connected to the DVR. That will cause a warning about not being a HD cable and asking to change to SD by holding down the EXIT. I use it all the time with my DVD recorder. Some people have done it by accident.
Depending on your TV the difference can be very noticeable.