Embodiments of the present invention relate to methods, systems and apparatus for controlling operation of a multi-phase machine in a vector controlled motor drive system when the multi-phase machine operates in an overmodulation region. The disclosed embodiments provide a mechanism for adjusting a duty cycle of PWM waveforms so that the correct phase voltage command signals are applied at the angle transitions. This can reduce variations/errors in the phase voltage command signals applied to the multi-phase machine so that phase current may be properly regulated thus reducing current/torque oscillation, which can in turn improve machine efficiency and performance, as well as utilization of the DC voltage source.