I haven't been able to determine the details of when this happens but when you paint multiple color zones (Extraction, residential, reforest, etc) overlapping multiple zones makes the other ... layers (?) colors invisible. For example, if you paint down residential+reforest+hunting, usually all you can see is hunting. (yellow) There's no true transparency after a certain number of layers.
I'm not exactly sure how you could designate that there are three zones in one space, other than maybe the border color including all colors.