Im using the most recent version on Steam. Says its 3.0.2. Anyway, I got a colony, the gold producing one up north, got the money to pay for weekly shipments of materials, messed around opening businesses on the mainland for a while, sailed back to build houses, had 50 in wood and stone, 40ish tools, and 650 food. I built a house, saved location and all that, opened menu, materials hadnt gone down, was confused, built several more, then looked, population cap hadnt increased either, materials hadnt gone down went to forts, built fort, materials went down, upgraded until i was low on materials, went back to menu, saw population cap had gone up, the cap had increased to 5. Stays 5 even if i destroy all the buildings now.
Edit: So, building wells increases population cap, not houses. Is that intended? the tool tip for houses says they increase population.
Edit: Im sorry, I just now found the thread about this from december.