dsmith, thanks for the effort of replying!
I'm aware of the difficulties of troubleshooting, especially problems that only appear briefly, non-frequent, randomly and non-reproducable. It's part of my daily job although in a different domain. I can confirm the solution to a technical problem is often found where it is least expected. I've had it multiple times we replaced all but one component in the chain, and the last one turns out to be the culprit.
The part about syncing the signal with PLL I understand, although I have difficulty imagining the problems we're seeing would arise from that. I've had the blackout's many times using VLC-player, I don't think the GPU clocks down or idles with VLC playing in a dual monitor setup (continuous video stream), with a bunch of other apps open at the same time. Okay, I know - there are thousands of other possibilities, you just mentioned that to illustrate the complexity, which I don't doubt, and it is indeed up to Apple & Intel to investigate, not us... agreed.
You lost me a bit with your anecdote about analysing transceivers with an oscilloscope, but hey, I get the picture ;-)
Thanks for the constructive thinking along.