how to calculate rms voltage value of PWM motor
for d=PWM duty cycle  for DC input \$ V_{rms}=d*V_{dc}\$ for each phase 


assuming half bridge drive between Vdc and 0V

Averaging DMMs assume sine wave and measure peak and convert and for a sine wave \$V_{rms}= V_p/\sqrt{2}\$  so your results will be in error with PWM and DMM and true RMS meter or correction factors must be used.