whole milk and diaper rash

I have a 9 month old and she is eating all table food no baby food. The last month or so she has really increased her formula intake to 35-40oz a day sometime she drank 45oz, plus eating for table food for every meal. She may eat alot but she is little (weighs 17.10oz). Her doctor said a couple weeks ago she should be down to 15-20oz for formula/whole milk by time she is 1 years and eating more and more table food. So about a week ago we (daycare and I) thought about cutting out her 3:00 bottle and giving her more of a snack and her sippy cup (that she FINALLY will take). We thought maybe putting 2-3 oz for whole milk in there would help get her use to regular milk. She didnt get milk every day, some days she was sleeping during snack time. The good thing is she liked milk but the bad news by Friday she noticed her bottom was very red and it had been like that off and on since MOnday and it didnt matter if you changed her as soon as she went potty her bottom was still horrible. She didnt have diahhrea but she did have more dirty diapers then normal. She does ok with cheeses and yogart. My husband thought Saturday that maybe it is from the milk but she drinks milk based formula and does fine. My husband isnt allgeric to milk but it does affect him, not cheese or anything just milk or ice cream. SO I stopped the whole milk all together and she hasnt has as many poops and she bottom is completely better. Could the whole milk be causing it? Why would she have a reaction to whole milk but not milk based formula? My mother in law said maybe she will have to be put on 2% in stead of whole, what is the difference? My husband had to be on Soy as a baby, but he couldnt take formula either. I always thought if you had a reaction to milk you would with cheese and other milk products. any thoughts.