When I use SCM Toolkit to change the colors, I use it as the last thing, before going public.
After the map is finished,,, by using editors.
Save it.
Use SCM Toolkit to change colors.
((You are choosing different color numbers I assume))
Save it.
If you go back into the editor to look at it, then change it, and then save, it can change the colors back to default.
But, I will admit, in a couple of maps the color changes just would not take.
You may be running into that, if so,,,,, new map time.