We played with it last night for a couple of hours, with 1080p resolution, and it worked perfectly. So I think it is pretty much fixed.
However, I discovered another oddity last night that is giving me some concerns; I have all my inputs to the Denon on HDMI, including my Cable DVR, my XBOX and my Oppo 980 DVD player. All are assigned appropriately in the Denon setup and I can play all of them just fine on main zone. However, on zone-2 I can select any of them, but no sound comes out. I can select the built in tuner and I get sound, but I can't get any sound from any of my HDMI sources.
Another minor annoyance is when you use the Tuner and you have the GUI displayed it does flicker quite a bit still, but this is not a big deal.