I thought I did this the last year this happened. However, I might have missed some items in your checklist. Will do it again. I thought exactly like you the first time this happened. So, I am happy that I was not imagining things.This sounds suspiciously like a hardware issue: a loose connector or a loose IC in its socket. I'd shut the thing down, and remove and re-insert every connector. If that doesn't work, do the same, and open up the case and re-seat cards, ICs, and cables. I'd also tighten up any screws.
Regards Ramesh