Multi-energy radiation sources comprising charged particle accelerators driven by power generators providing different RF powers to the accelerator, capable of interlaced operation, are disclosed. Automatic frequency control techniques are provided to match the frequency of RF power provided to the accelerator with the accelerator resonance frequency. In one example where the power generator is a mechanically tunable magnetron, an automatic frequency controller is provided to match the frequency of RF power pulses at one power to the accelerator resonance frequency when those RF power pulses are provided, and the magnetron is operated such that frequency shift in the magnetron at the other power at least partially matches the resonance frequency shift in the accelerator when those RF power pulses are provided. In other examples, when the power generator is a klystron or electrically tunable magnetron, separate automatic frequency controllers are provided for each RF power pulse. Methods and systems are disclosed.