Same thing happened to me, which is a good thing. origanaly the NPC's were suppose to have their own agendas not just wander around the same few tiles waiting to be hired or eaten up by monsters. I hope they keep this in, they should also be able to take over your towns if you leave them empty. However instead of killing them when you re-capture it, some shoul have the option of joining you. Wether they take it or not is up to them...
Also what the hell happened to fallen npcs? This was the first complait from beta testers when we realised that all the npc's were were bumping in to were human. Hopefully the community NPC pack will fill this void.