MTH engines and Atlas Switches

Sure sounds like bad batteries to me.

If these MTH engines are the ones using the "9 volt looking type" - temporarily try a 9 volt battery in place of yours. If they work, you'll know the cause of your problems.

MTH batteries act differently under load even if they are charged.

First, measure the distance between the pick-up roller assemblies on your model. Then measure the distance between the powered center rails at your atlas switches. If the distance between the two pick-up rollers is shorter than the length of the "power gap" in the Atlas switch, then the model will stall/stop/hesitate. I have an MTH steam locomotive model that did just that on all my Atlas switches, since the model did not have but two pick-up roller assemblies on the engine. I added a third pick-up roller on the tender and wired it into the power system, and the model runs fine now.