Perfect! You obviously know what you are doing, as so far everything looks right (connections, settings, tried different inputs made no difference, microprocessor total reset done, and presumably updated FW,.. etc.),so most likely there is something wrong with the HDMI board, at least regarding the HDMI 3 not working issue.
I know it is inconvenient, and the unit is quite heavy, but for such an expensive unit, imperfection is unacceptable. They obviously must fix the HDMI 3, possibly by replacing the whole board. The audio drop out issue may not be related to the HDMI board, being intermittent, it is important that you really emphasize the issue and insist on them letting you know what they are going to do about it, and fixed it so that you don't have to send it in the second time.
Such flag ship AVP are now getting ridiculously expensive, and that's why I replaced my 8801 with a C$1143 AVR-X4400H so that I can replace it every 2-3 years if I really want to keep up with the newest features, or not, without feeling much pain. In the US you get 5 years warranty but in Canada we only get 3 years. so that's any worry, and downside for the high cost AVP option. So far I found absolutely no audible difference between the two units. In fact the new AVR's (at 1/3 the cost) may be more accurate in bass response, post Audyssey calibration.
Best of luck![