Cool, I am getting much better results now. No error messages. I just set all my speakers to large and then ran the auto-setup. Maybe the defaults should be set to start with the all speakers to large (or better yet don't use existing settings when re-running the auto-setup).
Oddly though, the delays are all correct in distance except the center. It is reading 15 feet for the left and right which is correct, but it is setting the center to 3 feet. Maybe I have some weird reflections going on or something. It didn't seem like it ever did this before. I'll keep experimenting to see if I can get the auto-set right.