Okay, I've recreated the problem. I totally removed the 2 storey addition, and started from scratch. I added a one floor addition, but when I go to create a second floor above it, the system thinks I want to add a third floor. I'm attaching the plan as well as a screen shot of the message I get. I thought maybe it was because the addition shared the wall of the main house, so I tried sistering a wall so that the new room had four walls of its own, but I get the same message. And if I go ahead and let it build the new floor, it adds a new (3rd) floor to the whole house. So that's why I ask about making the addition independent of the main house - I can't seem to find a way to do that.
Kitchen Wing - 1.5 storey.plan