A linac-based X-ray system for cargo scanning and imaging applications uses linac design, RF power control, beam current control, and beam current pulse duration control to provide stable sequences of interleaved pulses having different energy levels, for example alternating 4 MeV and 6 MeV pulses or other energies where the difference in levels is at least approximately 1 MeV and less than approximately 5 MeV. The pulse repetition rate can be 100-400 pulses per second or more. In an embodiment, a cool down calculation is combined with automatic frequency control to provide stable energy and dose per pulse even upon restarting of pulsing after an “off” period of indeterminate duration.