I have the same problem, although my house is about 23 years old. I (and previous owners) have had the foundation propped up in places--this hasn't helped much with the settling. I've gone so far as to have a structural engineer out here. He said that no house is perfect, and it isn't as bad as a lot of them. There could be numerous ways to fix it....such as shimming up between floorboards and joists, etc. I think at this point I'm prepared to call it "character" and live with it.
Alas, but your house is new! I figure what you'll run into with your builder is he tells you basically to live with it. Especially if the substructure is sound. If he does say this, I know what you're thinking--"Didn't he just tell me that he was OK with mediocrity?" Maybe I'm wrong, but I bet he is....
Please keep us posted. I, for one, am very interested in how this turns out!
-k2 in Colorado