There is provided by this invention an apparatus and method for generating voltage pulses to first and second magnetron devices in a plasma chamber. An isolation transformer is connected to a pulsed DC power supply having a flux sensor, such as a Hall effect sensor, in close proximity to its air gap to monitor the transformer flux. A control circuit is connected to the flux sensor to control the duty cycle of the transformer by controlling the flux of the transformer such that the maximum and minimum peak transformer fluxes are equal in magnitude and opposite in sign to prevent saturation.