What meds is she on, what dose and how much does she weigh? From what I know lactose intolerance is very rare, but milk/soy protien intolerance (MSPI) is much more common and can be the reason for reflux. The symptoms you describe certainly sound like uncontrolled reflux.
Maybe it would be worth trying the nutamigen again, it may be that you need to wean her onto so she gets used to the taste gradually by mixing it with the formula she is on now and gradually reducing the ordinary formula while increasing the nutramigen.
Laura