Well, the club's president's SD70ACe had the same problem that you're describing. I'd hit F22 on my throttle, then hit F3, it would start up, and would work when I took the address out of my throttle so that he can pick it up with his (I use a Digitrax DT402D throttle, while the president uses the DT400) and run it just fine, but if the layout/block goes down due to a short, then it doesn't start back up while his other engine does. (He had two, only one had the problem. He has all three numbers now)
Here's a hypothesis, it's not backed up by any fact, but I suspect that the ProtoSound boards for HO, which are made in Thailand are very flaky and MTH is trying to not answer your questions so that when the warranty expires, they don't have to help you.
Give MTH a call. If they pick up, they won't be as willing to tell you off over the phone, or ignore your concerns.
Another member has a UP SD70ACe where the ProtoSound board burnt out. MTH said that the engine is out of warranty and that they can do nothing for him. He took it to an MTH authorized service center where they replaced the ProtoSound board for him. The board cost him $180 (that was the price of the board, the labor was free since it was a plug-in swap). He said that if he knew that it would cost so much, he'd rewire it for no sound and get another one with sound for another 40 bucks!