This comment is not a pile on but another issue I have seen with the new Atlas engines in reference to the PS3. There is a difference in the DCS signal strength/pickup as weaker in the new Atlas engines. The new Atlas engines have response issues on the layout where the older PS3 MTH versions don't.
I don't blame Atlas as they are just buying parts. It could be as simple as a change in component manufactures that have different tolerances. It also could be the engine has not as good of grounding and has nothing to do with the boards. I had a new MTH "shinny" Big Boy that had issues and fixing/adding grounds to the wheels resolved its issues so it would run/respond the same as the older versions of the Big Boy MTH had released. I have not had time to really look at the new SD70ace's to see why they act differently. On smaller layouts I'm not sure you will see this issue, but on large layouts where you are pushing signal strength, it will show up.