A method for processing a substrate in a reactor by pulsing RF power, includes: applying RF power in pulses in the reactor to process the substrate; monitoring data from the reactor indicative of anomalous pulses of RF power, including data from a photo sensor equipped in the reactor; counting the number of anomalous pulses of RF power in the monitored data; determining whether or not the number of anomalous pulses of RF power is acceptable; and initiating a pre-designated sequence if the number of anomalous pulses of RF power is determined to be unacceptable.