ben already stated this season that he stole alex, and that he was not really her father.

i believe jack is reluctant to be around kate and aaron, because he knows who claire is by then, and feels guilty that his sister was left behind on the island. but that is just a guess.

but i am almost positive he knows Aaron is his nephew, that is why he makes the comment at the end of the episode- "you are not even related to him" when kate tells him he can't be around "her son."