It does sound like the super cap that maintains power to the board after power loss, so that the board can do a proper shutdown. Isn't the super cap soldered to the board? There are several large capacitors on the board. Which one is the super cap. I would have a repair tech do this. Could the cap be tested by checking voltage across the cap immediately after disconnecting track power?
It could also be a software issue if the board is going through a proper shutdown. You could try reloading the software for the engine.
George