SW 2018 SP1
If I open the specific Configuration, then click the "ok" checkmark, I lose the color of my part. I only lose it when the color of the PART was applied. I played with it a little, and if I applied the color to a body, or a face, I don't lose it.
::I'm not sure if this plays a part in this, but I set the material before manually changing any appearances.
Also, I just modified a part. I changed the body color, and a hole face color (separate colors) when I opened the configuration properties, pressed 'ok', it added a color for the part, the default grey.