A power supply system includes a RF power source configured to generate an output signal at an output frequency, a signal source configured to generate a perturbation signal, an extremum seeking frequency controller configured to generate a frequency control signal based on the perturbation signal, and a frequency selector configured to select a perturbation frequency of the perturbation signal that is isolated from at least one frequency tone associated with the power supply system. The frequency control signal varies the output frequency of the RF power source. Other example power supply system, methods for controlling a RF generator, and control systems for controlling a RF generator are also disclosed.