a Franco-Iberian union? That's a powerful Popish stateSpain and Portugal are absent from the pedia as well.
I easily enacted the Aragon/Leon as Spain, as they were my vassals. France is very powerful but fortunately it cannot resist to a united Spain (not Iberia yet). Aragon and Portugal were my best friends and my vassals for most of the game.
Poland collapsed soon after its union with Lithuania (Krewo). I'm not sure it's related but it may be.
An issue I see with the France+Burgundy union is how powerful France would be if it won. In my game I had the luck of conquering most of Burgundy before the union happened so France got only Beaune.
I think corporations are flawed in their current state and should probably be changed à la Sword of Islam.
Finally, I had a python exception around 1526, for the Spanish Netherlands union:
Code:Traceback (most recent call last): File "CvEventInterface", line 23, in onEvent File "CvRFCEventManager", line 134, in handleEvent File "CvRFCEventManager", line 145, in _handleDefaultEvent File "CvRFCEventHandler", line 551, in onBeginGameTurn File "RiseAndFall", line 937, in checkTurn File "RiseAndFall", line 3373, in doUnions AttributeError: 'module' object has no attribute 'iUnionProvs2' ERR: Python function onEvent failed, module CvEventInterface
I played as Poland and the union of Krewo nearly collapsed me, it could have easily killed an AI.
The France Burgundy union happens at an appropriate time and the French completely came out ahead.
It appears that Novgorod is founded too early

If the primary country is master of the secondary country it should be automatic.
What currently happens when a third country owns both the primary and secondary countries (peace vassals), does it proceed as normal?