Currently in the 1.09n beta creating a custom faction works for everything but map color.  It is impossible to change the map color from its default, and it only seems to change when switching races.

When switching races it actually appears that the map color just matches the skin color of the currently selected race.  I'm reasonably sure this is a recent issue as I have other custom factions created before the 1.09n build without this problem.

EDIT: Strangely enough going back into the game (not restarting, just alt-tabbed to edit this) after posting this the color did in fact change and now matches the faction color.  Still cannot change it manually though, have to change the faction color for it to change the map color.