Started playing in 1.0, loaded that save game when I updated to 1.01.

Acquired (invaded) a settlement from a minor faction and after a few days population was 57/50 (when I look at the level 1 line it says the settlement will level up when the pop reach 50 ). After that no town leveled up. Same thing happened with one more settlement taken from a minor faction.

My bigger towns have a way to go til leveling up so at this time I don't know if this happens only for level 1->2.