Why does the CRJ100/200’s FMS miscalculate temperatures at altitudes in excess of 36k feet?
The reason is that the tropopause is at 11 km (36 089 ft) in the International Standard Atmosphere. At the tropopause, the temperature lapse rate of the atmosphere (how temperature changes with altitude) has an abrupt change: the ISA value is -6.5°C / km (-1.98°C / 1000 ft) below and then suddenly changes to 0°C / km (meaning temperature suddenly stays constant).
The FMS probably converts SAT to ISA deviation based on a fixed lapse rate of -1.98°C / 1000 ft, which means the conversion is wrong above that altitude. Only a Bombardier engineer (or someone involved in the Collins FMS used on the CRJ) could tell you the exact reason why. Based on John K's comment, it seems to have been fixed after the accident.
Note that the actual tropopause altitude can vary (usually between 9 km at the poles and 17 km at the equator).