Well, it may just be her physical type. I love milk and dairy products, but had late puberty and have always been very very skinny. I mean, many girls I knew started their periods around age 11 or 12, and I didn't until after my 14th birthday. Now, we did use powdered milk a lot in cooking, so maybe that invalidates anything I'm saying, but.... My older sister (likely) has a hormonal imbalance called polycystic ovarian syndrome (like my mother had), which among other things causes problems with weight gain. My sister has not been diagnosed, as far as I know, but her physical symptoms resemble my mother's and also those of several of my sisters-in-law, who have polycycstic ovaries. My younger sister is taller than I and even skinnier. So, it could just be your daughter's particular genetics.
If you want hormone-free milk, check out your local Braum's ice cream parlor, if you have one in your community. They don't add hormones to their dairy cows, and the price is comparable to grocery-store brands. (And I think it tastes better.) Something else I've heard but I've not read heavily about is soy - it's possible that soy products also mimic female hormones and so are not good in large amounts for young children, especially boys. And it's astonishing how many things soy products are in - not only most anything that uses oil, but also bread and cookies. But you'd have to research soy on your own to be sure, because I haven't read much on it specifically.
And little kids need the calories that come in whole milk until they're at least 2 years of age. And not just the calories, but the fat itself is necessary for the healthy development of their brains, because much of the brain consists of fats. They (and we) also need omega-3 fatty acids and DHA for healthy brains; these are found in animal products like fish and free-range chicken eggs (though "multigrain diet fed" chicken eggs are a decent substitute if you can't afford free-range). My husband is studying medical biochemistry in medical school right now and is telling me all sorts of interesting things! (Including that "partially hydrogenated" anything = trans fat, and they're really bad for you, so go off the ingredient list and not the nutrition label, because if a serving contains less than .5g of trans fats, then the company doesn't have to report it. And, high fructose corn syrup is really hard on the body, so try to find other sugars.)
Right, so not all of that is related to your question. But I hope something in there does help.