Sorry, I didn't your original question well enough.
On Atlas turnouts, there are 3 likely reasons for stalling:
1) dirty track. Not likely in your case since it happens at virtually all turnouts and crossings.
2) rivets and tabs are loose on the turnouts. A picture of your specific turnout would help in diagnosis because the design has changed a little over the years. In general on Atlas turnouts, there is a metal tab that electrically connects the closure rail to the adjacent stock rail. There is also a type of hinge - used to be a grommet - that hinges the points (parts that move) to the closure rails. These hinges have to conduct the electrical power. Again, it is unlikely that all your turnouts have loose connections at these places.
3) the insulated frogs. Atlas turnouts and crossings have plastic covered or insulated metal frogs with no power in that section. Chances are your switcher only has functioning electrical pickup on one or two wheels on each side, and that this wheel(s) are on the insulated section when it stalls.
Fixes for #3:
If your Atlas turnout has a metal, not plastic, frog - only a few do - it is possible to attach a jumper to the frog with a tiny screw. The jumper must go to an electrical contact that changes polarity when you throw the turnout. Caboose Industries makes a ground throw that has a contact built in for this purpose. Others put a slide or toggle switch in their throw mechanism by putting a wire through the slide or toggle switch handle to accomplish the polarity change.
If your Atlas turnouts have plastic frogs the only fix is to improve the pickup of your switcher - a good idea anyway. First, check the existing pickups. Are all the wheel wipers in place and making good electrical contact? Fix any that aren't first. Then add wipers to any drive wheels that don't have any. An alternative to wheel wipers is sliding shoes that lightly rub the rail. Ends have to be turned up so the shoes don't snag. The sliding shoes are a little more visible than wheel wipers but are a somewhat more reliable contact. If there is room, add weight to the engine. This will improve both pulling power and electrical contact. With small switching engines, there is no such thing as too much electrical contact.
Hope this helps more.