After train stops it can be left for a while and then it will work again. Is it overheating?
Sounds like something is resetting itself.
I suspect the transformer may be the culprit. Is it getting warm? I think the current Bachmann transformer is a big block wall plug running to a controller. Check the wall plug for heat. Unfortunately, the power supply that comes with the sets seems to have a voltage leakage, even when it is turned all the way to "0". I'm not sure how long they last. You might consider getting a new power supply if you can't figure out what is causing your set to stop.
1. When the locomotive stops, do the lights stay on?
2. If the answer to #1 is "no", Turn the locomotive over. Are the wires at the lead truck still connected? Perhaps one of the leads is coming off. I gave a Tweetsie set to my brother and that apparently happened.
3. If it is neither of those, perhaps it is the power supply.
If you have a Big Hauler train set, its most likely the transformer (power supply) is overheating. They are known to do this. LGB/Bridgewerks makes a 3 amp and Crest/AristoCraft makes a 3.5 amp power supply that would make a good replacement. There are numerous larger power supplies available too.
-Brian