So it only happens if you leave the player in the sled and then turn off the ignition, then turn the ignition back on again?

In other words, if you yank the player from the sled without turning off the ignition key, then put the player back in the sled, then it doesn't happen?

If so, I wonder if it's some new previously-unreported symptom of the negative spike bug ?

You said you already soldered in a new DC power jack, so I'm not going to try any troubleshooting down that road. Are the steps you described 100 percent reproducible, or is it intermittent? Intermittent results might indicate some kind of intermittent hardware issue (such as the DC power jack or a loose wire in the case), but you've been in there already, even going as far as fully removing the motherboard, so that's unlikely to be the issue.

How about This one? Again, doesn't really explain your symptoms, but worth looking at.