Power conversion systems and a controller thereof include a processing system that generates inverter switching control signals at a switching frequency, and transitions the switching frequency from a starting frequency to a target frequency over an integer number N blocks. The individual blocks include an integer number M subblocks with a starting frequency subblock in which the processing system generates the switching control signals at the starting frequency, and a target frequency subblock in which the processing system generates the switching control signals at the target frequency. The processing system operates the inverter at multiple demanded voltage values for multiple characterized switching frequencies, measures and records a corresponding inverter output current value for each of the demanded voltage values, creates and stores a lookup table for adjusted demand voltages at each of the characterized switching frequencies, and operate the inverter according to the adjusted demand voltages.