I wonder if the power supply is taking a while to become stable when the machine is first "switched on", either for thermal or capacitance reasons. The reset signal to the CPU will only work if the power supply lines are nice and solid at that time. On later machines, I believe, the reset signal is actually not generated until the power rails are stable, but on this one it just looks like a timer. I don't suppose you happen to have another one of these machines or a Plus do you? It would be useful to try this board out with another analogue board/PSU to rule this out