Shorts won't affect our reading, and generically, any early contact (before the intended tip junction) of the two thermocouple wires will lower the temperature, not raise it. So that's probably not it. An "open" will cause the reading to float around and be random / erratic. So that's not an impossibility. If you were somehow gettting an outside voltage onto either wire, that would cause a spike (but would be more likely to rail out, not just hundreds of degrees). Is it definitely correlated to the engine run speed? Any chance it has to do with electrical load changes as you shut down your electrical system?
Also, one thing to do is to move the probe to another cylinder and see if it moves with the probe or the cylinder, just to make sure you're not seeing an actual temperature spike (granted, 1200C when shutdown doesn't seem likely to be real)