We had a similar problem with our son, although the allergic reaction manifested itself in eczema all over and GI problems. But we tried EVERY formula out there when I weaned him (I had to be dairy-free while nursing him, but he never nursed very well, so by the time he was eight months old, I had to throw in the towel, as he was hungry all the time and not getting enough from me), and he couldn't even tolerate the regular soy formula--nor could he tolerate the super-expensive hypoallergenic formulas, which really surprised our pediatrician--she said they work for most kids. We finally found a solution that worked after months of trying: Baby's Only by Nature's One. http://www.naturesone.com/. For our son, we had to use the soy formula, but they have others as well. Turns out that while our son indeed cannot tolerate dairy, he was also having a bad reaction to the corn syrup that is in virtually every formula out there. Baby's Only is the ONLY one we could find that uses rice syrup instead of corn syrup--and the minute he was on that, he was fine. Might be worth a try. Whole Foods carries it in the store (at least in Sacramento), but you can also order it online. It's very inexpensive, which is a nice bonus--only about $11/can.
One thing to note: It's considered a toddler formula as opposed to an infant formula, but our pediatrician told us that was fine--that because we couldn't find anything else that worked, a toddler formula was far better than our son getting NO formula at all. (He was just shy of a year old.) May want to ask your pediatrician, but ours was fine with it--and just glad we found something our son could digest.
Good luck!!