Oh. You mean you want to know the reason? 
The track ground (black banana jack) on the DCS-RC is NOT the same as the internal digital signal ground as used by the microcontroller chip. I confirmed this with a DMM continuity measurement.
By peeking under the hood, there is a bridge rectifier which converts the track voltage (typically AC but can be DC) and converts it to DC for use by the digital electronics. So the track voltage "ground" and the internal digital signal "ground" are not the same. The signal transformer also kind-of sort-of corroborates this as this is in all likelihood how the high-frequency DCS watchdog signal is coupled onto the track voltage coming from a circuit with a different ground.
Not to worry. Just hook up a 25 cent DC-optocoupler and a 5 cent resistor between your Arduino output pin and the DCS-RC. If not familiar with this interconnection technique, I can draw you a diagram/schematic. If you don't have these parts lying around, it will be annoying since the shipping will be 10 times the cost of the components. 
Actually, you could connect the Arduino ground to the DCS-RC internal ground rather than to the DCS-RC track ground. You would not need an optocoupler and could directly connect the Arduino output pin to the DCS-RC reset pin. Everyone is entitled to their opinion; my opinion is you should NOT do it this way...please use the optocoupler method.
But moving on. So every time you trigger a relay to power up a previously unpowered siding, issue a reset pulse to the DCS-RC. The pulse should be, say, 0.1 seconds long. Do this 3 times (or however many you want) with each pulse separated by 1 second. Note from earlier discussion that the DCS-RC sends out the Watchdog burst about 3/4 second after you issue the reset pulse. The duration of the Watchdog burst is very short - less than 0.1 seconds IIRC.
