it seems to happen when the turnout side of the truck of cars are bridging the points of the switch
It is a short, but 1. all Atlas switches' point rails match polarity with it's stock rails. and 2. few cars today come with metal trucks. Do you have Metal wheels?
If so, are they in gage? There is also the possibility that your short is occuring elsewhere. 6 wheeled trucks seem to have problems over too sharp switches, and Atlas 'Snap' switches are sharp.
I think that one of your cars is SUSPECT and needs re-gaging the wheels with an NMRA gage. I also think your short is being caused by something else.
What happens when you isolate this car from the rest? Run it back and forth by hand over the trouble spot, with power ON. Turn off the lights at night to see what sparks..
ISOLATE the problem. Is it the car or the switch? - The truck or a wheel? (Could be a coupler problem).
Lots of things need elimination systematically here. If the trucks are indeed metal, is one side frame journal sufficiently worn that a metal wheel is actually rubbing on the inner side of the sideframe? Could be cause for a short there if the frame also touches the loco frame...there's more to that, but at least it is a possibility.
I do agree that the chances are excellent for it to be a metal wheel tire actually making contact with two electrically mis-matched rails at the frog-rail separation. That's the same as having a wire or a coin across those two rails.
TenX,
The Atlas 'Snap Switch' has long plastic frogs, so I do not see even 'wide' wheel treads bridging and causing a short(like with Peco Insulfrog turnouts). The point end is also quite 'short proof' - the stock rail and the adjacent point rail have the same polarity. The Atlas turnouts have a very wide gap there as well.
If you have metal truck sideframes, and metal wheels, maybe an uninsulated rim might be touching the sideframe. Also if you have older cars with metal frames, you could produce a 'short' if the insulated wheels on one truck are on the right, and the other truck has them on the left. I had an old 50' gondola with metal wheels/trucks/frame. I got the trucks turned around and problems started. The car did not really short out the rails until it ran a few laps and the rubbing of the bolsters finally produced a short circuit through the long metal frame of this plastic car. I took me all Saturday afternoon to find the car!
Jim
Modeling BNSF and Milwaukee Road in SW Wisconsin