A data reduction process for a temperature sensitive paint heat transfer measurement system in use at the US Air Force Hypervelocity Wind Tunnel No. 9 has been evaluated using a set of data gathered from tests on a generic hypersonic waverider model. Discrepancies were observed between heat transfer results calculated using temperature sensitive paint based measurements as compared to results calculated using conventional thermocouple measurements at specific locations on the test article. Paint thermophysical property estimates were made and utilized in a series of finite element models to analyze paint behavior. These models were used to perform a sensitivity analysis on system parameters. Key identified parameters were used to perform a non-dimensional analysis of the tunnel data. Based on this analysis, discrepancy areas were identified and a novel two-calibration data reduction process was developed that mitigated the severity of some observed discrepancies and showed the potential for future improvements.