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The photos on the page you linked for the MD board appear to be a duplicate of the original boards used.

Having said that, irrespective of your control problems, please verify that the system will shut the track power down with an overcurrent condition. Simply temporarily short the track, and if the MD you have has current feedback, the Arduino will shut track power off, and the red LEDs will shut off.

Once you do that we can figure out the control problem.
 
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