At the beginning of this episode, the best practice to determine the source of the problem would have been to use a voltmeter and go from the middle rail of the main line to the middle rail of the siding, to see if there was a difference in voltage. Then you could have traced that difference backwards towards the source(s) of the voltages.
Using a consistent system of color-coded wiring will also help in trouble shooting a suspected reversal of polarity such as this. The convention I use is black for the outside rails, brown for an isolated rail used to activate an accessory or relay, white for isolated returns, and all the other colors for "hot" wires.
