Why does the CRJ100/200’s FMS miscalculate temperatures at altitudes in excess of 36k feet? The CRJ100/200’s flight management system (FMS) apparently is not to be used to calculate engine thrust settings when the aircraft’s altitude exceeds 36,000 feet, due to internal calculation errors at altitudes this high:

The Pinnacle Airlines CRJ FCOM, volume 2, Performance, pages 50 through 52, dated June 2002, presented altitude and climb capability charts. Pilots were required to consult these charts anytime a flight was operating above 36,000 feet because of a flight management system (FMS) limitation above that altitude.77  [...]
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77 FCOM volume 2, Operating Limitations, pages 30 and 31, dated June 2004, stated that “the FMS calculated thrust setting must not be used if the pressure altitude is greater than 36,000 feet.” The Bombardier chief pilot stated that the reason for the FMS limitation above 36,000 feet was because of the inaccurate calculations above that altitude. Further, according to Bombardier, at altitudes above 36,000 feet, the conversion from static air temperature to the International Standard Atmosphere (ISA) deviation is incorrect within the FMS, resulting in an error in the N1 indication at those altitudes.  [...]  Bombardier’s Flight Planning and Cruise Control Manual and Quick Reference Handbook contain charts that show the proper N1 indication for altitudes between 36,000 and 41,000 feet.  [NTSB/AAR-07/01, page 33 (page 45 of the PDF file); footnote numbering in original; my emphasis.]

Given that 36 kilofeet is well below the CRJ100/200’s maximum operating altitude,1 it seems surprising that the aircraft’s FMS was not programmed correctly for altitudes beyond 36k feet, that this wasn’t caught very early on, and that the FMS  software was not updated to correct this bug once it was discovered; why was the FMS misprogrammed in the first place, and why wasn’t it fixed?

1: The maximum operating altitude for first-generation CRJs is 41 kft, a full 5,000 feet higher.
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).