First off - I don't know anything about your PC board.
I assume the PC board internally uses DC, and thus would have a half or full wave rectifier to create the DC from the track's AC. It would appear to me that there is a cap in the AC to DC conversion/regulation process that is taking a long time to charge, charge to a voltage level which is an operable DC level for the PC's electronics. So what may have changed? To change how long a cap takes charge, you control the energy being supplied to the cap by either changing the resistance between energy source, or how strong the energy source is.
Without a schematic, I would try to reverse engineer the PC a bit to see where the half or full wave rectifier is, then try to make sure all the diodes in the bridge are working. I would try to determine if there is a resistor between the bridge output and the cap, and make sure the resistor is within value. I would try to make sure that the center rail pick up to bridge, and bridge to engine frame-to wheels-to outside rail, are near zero ohm paths.
Wish I could be of more help!!
