I could pinpoint it to "Start with Player Colors on". If that is selected, every unit in the game will be black after a new game. Friend and Enemies. That was 100% not the case before the last patch(s). I reinstalled the mod again to be sure.
It saved me for every game two thankful clicks, because I always play with those colors enabled.
If they can not reproduce that bug in that way, then something is really odd.