Hey Wiz, thx for the great mod.
I think i figured out why the unified region modifier appears, and sometimes dosent.
If I take a whole region all in once peace settlement, i inherit a region that allready has the unified modifier. I think when the game tries to give me the unified region modifier, it instead takes it off.
For example: I conquered in order Bonnonia, Insubres and Salassi in the same war BUT annexing them at different times. A couple of months afterwards, the unified region modifier appears.
In that same war, i annexed the 2 provinces of Liguria, whom allready had the unified region modifier. At the same time I gained the Gallia Cisalpine modifier (explained earlier), I lost the Liguria modifier and it never came back even many years later.
In a previous game, the same thing happened with Corsica and Sardinia...
Hope this helps and you can fix this.
EDIT: I inherited Massilia's 2 provinces, gaining the whole region simultaneously. The region had the unified modifier, then lost it a couple of months later never to come back, confirming my theory.