Also consider this, some babies/toddlers aren't allergic to milk, and won't show up in any allergy test, but they are intolerant to it. Intolerances will not affect IgE at all, but all the symptoms will be the same. Even if the test result shows she is not allergic, she could be milk protein intolerance. Same symptoms, same end result, same form of treatment, just affects the inside of the body differently. No matter what, at least YOU know that she cannot have milk. I doubt it is a coincidence.
My son's symptoms cleared up on Neocate, but the scratch test and the blood RAST test showed no allergy to milk or soy. It just clarified to us that it is for SURE Milk/Soy Protein Intolerance. Either way he couldn't have milk and that was good enough for us. I wouldn't worry about the IgE levels. That's just one of many symptoms/signs. At least your doctor is aware of that and is smart to keep her on that formula.
When my allergist was trying to explain the blood test results he said as well that they are not very accurate as it can depend on the levels in that particular blood they withdrew. My son reacts severely to oats/barley, but his RAST was 1.5, whereas his result for egg was over a 5, but he only has a mild reaction. Just goes to show that the numbers aren't always the best indicator.