Go into the room DBX for those two small rooms where you built the walls and check that the floor structure is the same as the rest of the house on that floor. My guess is for some reason that floor structure in those two little rooms is different which makes them frame differently. Also make sure those rooms are on the same framing group as the big room surrounding it.
That's just a guess though. If not the problem then post the plan please.
misterwiley's post in Framing, Auto Generating Clear Spanning Floor Joists - How to ignore walls above during auto framing? was marked as the answer