Not to jump on the obvious, but do you know for sure what address the loco is set to? Most off the shelf decoders come set at address03, but most reset it to the road number of the loco. But I'm sure that NCE touched on that in the phone call, their customer service is exceptional.
It was a bad engine decoder. Iron horse hobbys in reading checked it also. They called atlas and they replaced it with a new one no charge. So all is good again. Just got in from 1 till 7 at hobby stores. They should close them all. Spend way to much money for all the neet stuff they have.