I just tried the Tory and Indian War 3 factions. It does not work.
This SC should explain it all
Long story short : The Americans like the Indians and would never harm them. The vile English are attacking the Indians at every opportunity, sieging their villages and in general behaving like very nasty persons. One American and one Indian stack in the same area ? "Hello, do you this fine leather jacket ? Homemade ! Support local initiatives !" One Indian and one English stack in the same area ? "DIE, HERETIC !" The Indian villages are not considered as owned by the Americans, though, even when a stack is on it.
I am not sure it should work like this. I have got the version 1.07b, and (this might be useful to know) Pontiac's War installed.
