I've only seen this problem with my regular O scale engines where they needed to be reset right out of the box, even to run in command. As far as I know, they worked from then on. I don't run conventional very often. I believe there were 3 in a narrow time frame for me. One of those got scrambled in a lash-up build. The most recent ones I've got, have run fine in command as is.
I think this engine has a special PS3 configuration with smaller caps, from what I've read in posts. Seems odd that it would need a reset each time though?