Which is why I suspected it was power related...It always happens on first cold boot (after night in the morning)
Though what Areca mentioned sounds like a timing issue (and I suspect that's the case), it could still be power related. Specifically, the capacitors (PSU, mainboard, ARC-1231ML) need time to charge (data is sent later than the system is supposed to receive it due to insufficient power to generate that data). It's a very brief period of time by human standards (ms), but if something isn't ready when the clock cycle hits, erroneous data results, and all hell breaks loose.
In such a case, a restart would work, as the caps are already charged on the second attempt to boot the system. What happens, is capacitors drain out over time, and won't contain sufficient energy on the next clock cycle unless they're charged again before the next clock cycle is reached. So when you turn off the system, the capacitors are discharged below the threshold value (minimum needed for the circuits to operate correctly), and you get this particular error.
Since the restart works, this is the most logical explanation based on experience.
As per a solution, you can either boot it twice in order to get the card running at x8 lanes, or leave it on over night.
Either way works, and is simple enough that either the additional aggravation or power consumption should be an acceptable compromise.
