Current protocols for the measurement of proton dose focus on measurements under reference conditions; methods for measuring dose under patient-specific conditions have not been standardized. In particular, it is unclear whether dose in patient-specific fields can be determined more reliably with or without the presence of the patient-specific range compensator. The aim of this study was to quantitatively assess the reliability of two methods for measuring dose per monitor unit (DIMU) values for small-field treatment portals: one with the range compensator and one without the range compensator. A Monte Carlo model of the Proton Therapy Center-Houston double-scattering nozzle was created, and estimates of D/MU values were obtained from 14 simulated treatments of a simple geometric patient model. Field-specific D/MU calibration measurements were simulated with a dosimeter in a water phantom with and without the range compensator. D/MU values from the simulated calibration measurements were compared with D/MU values from the corresponding treatment simulation in the patient model. To evaluate the reliability of the calibration measurements, six metrics and four figures of merit were defined to characterize accuracy, uncertainty, the standard deviations of accuracy and uncertainty, worst agreement, and maximum uncertainty. Measuring D/MU without the range compensator provided superior results for five of the six metrics and for all four figures of merit. The two techniques yielded different results primarily because of high-dose gradient regions introduced into the water phantom when the range compensator was present. Estimated uncertainties (approximately 1 mm) in the position of the dosimeter in these regions resulted in large uncertainties and high variability in D/MU values. When the range compensator was absent, these gradients were minimized and D/MU values were less sensitive to dosimeter positioning errors. We conclude that measuring D/MU without the range compensator present provides more reliable results than measuring it with the range compensator in place.