A method and neurostimulation system for treating a patient are provided. A plurality of pulsed electrical waveforms are respectively delivered within a plurality of timing channels of the neurostimulation system, thereby treating the patient. Sets of stimulation pulses within the pulsed electrical waveforms that will potentially overlap temporally are predicted. Stimulation pulses in the respective pulsed electrical waveforms are temporally shifted in a manner that prevents overlap of the potentially overlapping pulse sets while preventing frequency locking between the timing channels.