That is a switching power supply. What happens is that with the original Williams power supply, the large capacitor on it will continue to supply power to the CPU for several hundred milliseconds. In the meantime, the unregulated power will drop to zero, which invokes the CMOS memory protection circuit. The power supplies do this because the old Motorola CPUs (6800 & 6809) had a tendency to write randomly through out the memory space when the voltage dropped below a certain threshold. This includes the CMOS memory space.
Switching power supplies (including yours) do not have that reservoir of power to keep the CPU alive until the CMOS protection kicks in (both +5V and +12V go down at the same time) so as it is being shut off the CPU can randomly write garbage to the CMOS.
It usually doesn't overwrite the settings unless the memory protect switch on the coin door has been defeated or is missing. There is a seperate protection circuit for the factory settings part of the CMOS address space, but I have heard that some boards have a hardware bug that cause the factory settings protection not to work.
The easiest way to fix this is to go back to an original power supply. If you have the original board and it is not working, I rebuild PS boards for $20 + shipping. If you need a rebuilt PS board, I sell them for $30 + shipping.
The other way to fix it would be to build a board that sits on the PS cable and provides enough capacity to keep the CPU running until the memory protection kicks in.
Or just live with high scores and setting being reset.
ken