Yes, the ground thingie(s). I would like to think this was caused more by something connected that shouldn't be rather than the other way around. However now we know that what fried was a protection diode. Could it have been across what was suppose dto be 3.3V but was 5V ? What would they have in there, a 3.9V zener ?
If I did the math right, feeding a 3.3V device with 5V would result in somewhere aroung 2.3 X the power dissipation is it's analog. Digital may be a bit different, I would think lower, by that I mean a slightly smaller increase in dissipation. This because for the most part heat in a digital device is from the saturation voltage of the semiconductors and the capacitive load on anything that switches.What this all means I think is thast a 3.3V device wil actually work on 5V for a while, how long depends on alot of things. If the components just barely meet spec, minutes or hours, but if you happen to have a really superior specimen, who knows how long it may work, years even.
If a similar diode exists for the 12V suply, it is probably 15V, which means one volt will not bother it. In fact driving a motor, it might just be fine with an extra volt, but the next standard zener value up from 3.3 is 3.9. One volt is too much.
So if somehow a negative 1V somehow got on the commons, this would explain it. But then how would that thappen ? Concievably if it were an open circuit and chassis ground made that connection, even though it's a bit far fetched as it assumes quite a bit of resistance in that ground. It could happen though, with the uPrecessor drawing alot of amps during bootup. Something like this may actually require a chain of partial failures, just to make that one volt.
I agree that this is an intersting subject because the actual cause seems to be elusive. If we don't know why it happened this time there is no way in hell of keeping it from happening again.
J