I'm keen to get more detailed information on this. That seems very strange and certainly requires further investigation. However given your issue occurred on an AutoCal unless you know your tuners Software versions used with his v2 to create your tunes along with the AutoCal details it will be a task for your tuner.
We would need to know version details for both devices, full or calibration only flash, the exact steps followed for the flash (the more detail the better), the year of your vehicle, and a history - have use used other programmers and did you ever have issues? The replacement ECM was it flashed by TIS first? Did you read that controller before flashing? Did you check the SN before flashing? Etc.....
There is a process on the front page of our website detailing how to log a support case. You or your tuner need to follow that process. At this point we won't require trace files, but may request them of you as the case progresses.
Cheers
Cindy