I hope this helps you understand my layout better.
Two circles that cross each other I believe we'll call a figure eight. Shouldn't be too hard to figure out where your problem is, right now I'm leaning toward the Atlas selector switches and not the wiring itself, but then again anything is possible, including deposits on the loco wheels and track.
Clean the track with a rubber eraser and also the loco wheels (there are better methods but this will do for now), if the train runs good then that is where your problem is.
If it still stops then we'll have to look a little closer to the wiring.
It is also better not to depend on rail joiners to deliver the current to the track. Oxidization can build up on the surfaces an act as an insulator.
1. How are your wires to the track connected? Soldered? to track, rail joiners, etc.
2. Do you have a voltmeter? If not a 12 volt bulb with 2 leads will do
Run your train , and when it stops, use the voltmeter or light to check the track where you are losing the voltage, if the track doesn't have the voltage, then the next step back would be to check the Atlas selector switch . But try cleaning the track and loco wheels first.
Willis