While the IOBoard signal is 0V/12V, incandescent lightbulbs would die quickly if they were to be turned on and off this much. For that reason the power distribution board inserts a series resistance of approximately 850 ohms when the lights are commanded off. This generates a keepwarm voltage providing ~14 mA of short circuit current and the signal becomes 0.13V/12V when loaded with an incandescent lightbulb.
For that reason, replacing the lightbulbs with 12V LEDs make the buttons always lit because the additional series resistance provided while the lights are commanded off is not enough to sufficiently reduce current flow to the LEDs and completely turn them off.
The keepwarm voltage is generated by 9 resistors on the power distribution board labeled R1 to R9, one for each button. The 12V goes through the resistor before being sent to the lamp so there's a constant ~14 mA from lamp to ground. When the IOboard commands the light on (i.e. bypassing the series resistance), the lamp gets directly connected to 12V.
You can either desolder these resistances from the power distribution board, or bypass by wiring CN2 connector from BemaniPC side directly to the plugs which goes into the CN8 connector on the power distribution board (see above picture, unplug the circled 11 connector from the power distribution board, then plug dupont cables directly inside that connector which runs straight to the control panel lamps).