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 electrical waveforms that will potentially overlap temporally are predicted. Each of the potentially overlapping pulse sets is substituted with a replacement stimulation pulse, such that each replacement stimulation pulse is delivered within at least one of the respective timing channels, thereby preventing temporal overlap between the stimulation pulses of the respective electrical waveforms while preventing frequency locking between the timing channels.