I've had a similar issue with Auto calibration, where within the first 5min of operation the sensor temp and auto blackshade setting were such that the noise was much stronger than usual, but then as I was investigating it, the camera came up to temperature and the camera automatically switched into a different calibration setting and the noise suddenly disappeared. The big problem with this is that the camera doesn't change calibrations while rolling so if I were to have rolled in the first 5 min of the camera being on I could've had a screwed up noise pattern that might have even gotten worse due to further calibration mismatch as the camera gets hotter on all my footage no matter how long I rolled.
One consideration is that it may be nearly impossible to build a calibration that accounts for the sensor temperature that exists during the few minutes it takes for the camera to get up to temperature since the calibration process takes so long. Perhaps auto calibration can't really account for different sensor temperatures because it does not have access to them.
Moral of the story is maybe don't ever roll until the camera has been on for a few minutes or you may ruin your footage. I hope there is a way around this. This is a strong argument against swapping batteries right before roll...
I wonder how other manufacturers handle this.