The article presents an on-board power system designed for ships, aviation, and space vehicles using energy from photovoltaic panels. The power structure includes both DC and high-frequency AC power buses. As a result of pulse loads, this system is exposed to disturbances that cause electronic systems to reboot. To reduce the effect of the appearance of secondary disturbances in the AC bus to which the photovoltaic converter is connected, a new control strategy has been proposed. This strategy improves the operation of the proportional resonant regulator that controls the AC bus current by making the reference values linearly dependent on the DC bus voltage. A prototype of such a system was designed in the laboratory. The FPGA control board was pulse-disturbed, leading to start the auto-power procedure, and additional disturbances were observed in the AC bus for the standard system. Reduction in the impact of these disturbances was achieved using the proposed control method by reaching a limitation of the bus current in dynamic states caused by the auto-power on process from 280% to less than 100% of the steady-state value. Experimental results verified the validity of the proposed method.