Are you speaking of the "Auto" Thermal calibration setting in the Thermal preferences? Choosing that setting will cause the thermal camera to "self" calibrate at intervals during thermal usage. You will see "pauses" in your video feed. It will do this to try and prevent any blurring or resolution problems with your thermal IMAGE, not the temperature. I believe this is called geometric calibration. It will NOT mess with your reflective temperature setting or emissivity. Those should be set by you according to the project and material you are scanning.