Cohesion wise, militia are not being properly penalized for being out of state. In fact, militia outside of their home state have 5 more max cohesion than those who are at home. Discipline and movement penalties for being out of state are working correctly, it is only the cohesion.
The source of this bug is located in the GameLogic.opt file. Under the Home Area Penalty/Bonus there is this entry:
areaOutsideHomeTQ = -3 // TQ (and 5 time that to max cohesion)
This value is producing a positive instead of a negative (only for cohesion, not TQ). I verified this by changing the -3 value to -15, the result was an overall increase to militia of 60 maximum cohesion points. When I changed the value to a +3, it gave the proper result of in-state militia having 10 more max cohesion than out of state militia. However, the discipline value was not decreased for being out of state.