An actuator in an HVAC system includes a housing, a motor, a hub configured to receive a shaft, and a processing circuit. The processing circuit is configured to operate the actuator in at least a first speed mode and a second speed mode that is faster than the first speed mode. The processing circuit is further configured to perform a calibration process for the actuator. The calibration process includes temporarily shifting the actuator from the first speed mode to the second speed mode and driving the shaft through a predetermined sequence of positions with the actuator in the second speed mode.