My ds (who's now 23mo) went through something similar. He had a cow's milk protein allergy when he was younger. He was breastfed until a year and I became pregnant again. So we put him on a soy formula, and gradually introduced cow's milk to him again. He did fine with it and was also able to eat cheese, yogurt, etc.. Then suddenly a few months back he came down with a bad case of diarrhea that lasted about a month! But he wasn't sick otherwise. And like your lo, he had a terrible diaper rash that wouldn't go away. His doctor told us to take him off all milk and dairy for 2 weeks, then re-introduce it to him slowly, which we did. We gave him back cheese, yogurt, etc. and he was okay. But as soon as we gave him back cow's milk, he got the diarrhea again!
So, it might be a slight bit of a cow's milk protein allergy that your lo has. Can you have her tested? That's the sure fire way to know if that's the problem. You might have to go to a soy formula, or some other form of milk (rice milk, or even soy might be okay since she's just about 2) for awhile, until she's showing no sign of allergy.
I hope she starts to feel better soon!