Have you ched the ribbon cable?
In fact, it seems that the ribbon cable is likely to be much of, if not all of, the culprit. We replaced the motherboard and the HDD, to discover that the "Prototype KCP" issue persisted. Then we went back to the original HDD with the new motherboard and the problem persisted. (This config was tried because the old HDD worked fine in the full CPU package from one of the other robots).
We went to the boneyard and installed some old ribbon cables and the system has been working since.
The next time that this robot has a few days of downtime, we are going to put in the old motherboard along with the original HDD and the swapped out ribbon cables to determine if the old motherboard ever had a problem to begin with.
I'll post a final note to close this out after we have done that.