Is that one of the Atlas factory boards that has the "jumper" on top that you move from one set of pins to another to change from dc to dcc?
I picked up an Atlas SD35 at a train show that had one of those boards in it.
It ran the locomotive, but produced a significant "hummm" in the motor while doing so.
I ended up changing it out for a 3rd-party controller, after which the engine ran much better.
I recently tried the same [Atlas] dcc board on another engine (Proto 2000 GP38) to see if it would work, and again -- ran the engine, but same "hummm".
I'm wondering if this was characteristic of older Atlas dcc decoders?