I did indeed try that and set the priority to # 1 with the same erratic result. I have also noticed that if a show is set to record at the same time as the auto-tune that the show will record but the auto-tune will fail. I have the show start a minute early so there is no conflict with the processor trying to do two thins at the same instant.
I have CNN come on at 6:00 AM so I can scan through it in bed and it is on 200. Modern Marvels is also on at 6:00 AM weekly and I record it but it starts a minute early. MM will record fine but 200 is a bust ... every time. 16 tuners seems to really mean one tuner in this instance. I now wish I had my Hopper 2 back.
Yes, I have encountered your problem ONLY when a recording and an Auto Tune are set for the same program BLOCK regardless of being a minute before etc. I have found that you need to CHOOSE between either a DVR (recording) or an Auto-Tune, but you can NOT have BOTH. Pick the ONE that best suits your desires. Apparently the Dish DVR's do NOT seem to like BOTH Auto-tune and DVR for the same program scheduled at the same time. It is what it is, unfortunately. I think any of the engineers believed that people either wanted to DVR a show or Auto-tune to it, not both, and so the coders had no emphasis on this. It is just the way engineers think and coders prefer not to deal with the clashes and inexplicable problems it MIGHT produce.
I consider this something like Dish DVR's will not save programming streams in the buffer when viewing a DVR recording. My TiVo's do, but SO WHAT! Such buffering while watching a DVR recording is hardly a deal breaker, and I have perhaps 3 or 4 times in over 10 years of owning TiVo's ever benefited from the TiVo buffering while I watch a DVR recording--but TiVO only buffers for 30 minutes, while Dish buffers for an hour, and I have benefited from Dish's ONE-HOUR buffering far more frequently than TiVo's buffering while watching a DVR recording.
In my case, unless I don't care if I miss any portion, I just select DVR because I can always tune to that channel anyway, and most often it is the stream that is recording in progress and I can just REW to the beginning really fast, and it has the advantage of still being recorded if I choose to see it later.
I only use Auto-tune for events that I just don't care if I ever see, but for events that would be NICE to auto change the tuner if I know I am watching something I don't care if it is interrupted by an Auto-tune, but if I care to see such a program, then I DVR it and I happen to be someone who often goes into the TV Status (IIRC) screen that shows me all my tuners and what, if any, are recording or tuned in order to be aware of wanting to watch something currently recording (in progress). Checking TV Status is a GREAT habit of mine that makes me aware of recordings in progress I want to view NOW.
I hope that helps.