How are you converting the PWM output to control your motor? I assume you don't have a spindle speed sensor so the system is open loop. There needs to be a calibration adjustment in hardware between the PWM smoothing and the speed controller. PWM base frequency is not directly related to spindle speed, it's just the frequency of the pulses whose pulse width is controlled to indicate the desired speed. Normally you smooth those pulses to generate a voltage, which is scaled for calibration purposes, then applied to the speed controller.