When I typed "they poked in a FLIR camera pointed at our prototype's enclosure" I meant that literally: They cut a hole and pointed the FLIR through it. No "window" material to affect the measurement.
OK, logically your answer makes sense. In the IR, given STP and typical humidity, the intervening air should not affect the FLIR's measurement of a remote surface. That removes this possibility.
More likely, then, that my basic presumption is valid: The air warms faster than the enclosure, and what the the FLIR is actually measuring is the enclosure temp while our thermistor is responding to ambient air. The "thermal delay" of the thermistor is estimated by its manufacturer to be ~6-7 seconds (lots of possible variables but I presume this is based on the mass, thermal conductivity, and surface area of its bead with some allowances for heat sinking through the leads). The "thermal delay" of the enclosure is likely to be substantially greater given its much larger mass, so our thermistor reacts faster to the ambient rise (and our circuitry responds) while the FLIR reports the lagging indicator of the enclosure temperature.
I'll try to get them to measure the actual AIR temperature with an appropriate sensor.
Thanks!