I notice that you've soldered your rail joints, which is good, but you might want to clean the solder fron the top of the rails to lessen the chance of it causing a derailment.
I believe that Atlas crossings are powered on all rails at all times: is the crossing new? If you have a continuity tester (if you don't, get one) you can check the crossing to see if it's at fault. They're cheap, maybe a couple of bucks, and very useful for finding out what's not working in a situation like this. Shut off the track power when using it. The tester consists of a tube, big enough to hold an AA battery, with a flashlight bulb in one end and a probe. On the other end of the body is a wire with an alligator clip on the end. If you touch the probe to the clip, the bulb will light (because the circuit has been completed). Attach the alligator clip to one of the rails at a point where the locomotive was running okay, then touch the probe to different points of the same rail as it passes the crossing. Repeat this for all rails. If the bulb lights, that part of the crossing is powered: if not, look for a bad connection somewhere between this point and the last point that you checked which was working. If all of the rails show continuity, then the problem must be in the loco.
One other thing: I notice in your photo that there appears to be a piece of ballast stuck in the flangeway of the lower rail passing through the crossing horizontally. Any chance that this could be lifting your loco enough to cause it to lose electrical contact?
Wayne
