Ok, so we're looking at an enormous and deeply disruptive migration to the new world almost immediately after its discovery backed by extremely strong national governments represented not only on the Atlantic coast but on the Medeterranian as well.
I can think of why this won't work as an alternate history, but instead I'll turn this into a series of adventure seeds:
- A foreign ship is blown ashore and wrecked essentially on top of your settlement. A force is sent to ensure military safety. The force has the opportunity to save lives, especially those of women, children, and other civilians. Do they? If the commander gives orders one way or another, will they be followed?
- The year's crop fails right as the home country sends another batch of travelers. There is not enough food to go around. Some talk of raiding neighbors for food. Some talk of kicking out the new comers. Some hope to beg for grain supplies. Others say the town must disperse to communities that can feed themselves. Difficult decisions lay ahead.
- A local community ruler demands that his citizens spend 1 day a week toiling in the newly discovered mines. The conditions are terrible, but he's the highest authority, and to even complain about it is to risk a flogging. Even if the citizens could reach a higher authority, would the simple letter sent be enough to stop his abuses?
- Through some sort of mixup, a technically allied community with a foreign language is set up WAY to close to an existing settlement. Tempers are flairing, and most disputes are unable to even be resolved by yelling at each other. Fists and rocks have flown, and who knows what will happen next.
- Orders from some theorist in an ivory tower have commanded the settlement of what looks like an ideal spot, but is actually a festering swamp.
- The local governor is selling off supplies meant to keep colonists alive, leaving everyone else hungry.
The colonists here can't leave, are torn away from their traditional support structures, have limited ability to appeal decisions, and are part of a very hierarchical system. That's really close to slavery. You've got a very top down system, and the potential for abuse of power is immense.