We had a lot of problems when we switched our daughter to milk-based formulas and then to whole milk. Mostly rashes and digestive problems. Lots of diarrhea and bleeding rashes in her diaper area. It turned out to be just a sensitivity to a protein in the cow's milk that she couldn't digest.
We consulted with the pediatrician and he suggested soy milk. We kept her on soy milk for nearly a year and then gradually started trying her on cow's milk again. She grew out of it and now loves to drink milk.
Ask your pediatrician and be make sure that they listen to you. Describe what happens, the gas, any bloating that you notice, and anything that you think is important. It will help them make a more accurate diagnosis. If it helps you to write down everything and then bring in the list, then do it. I find I tend to forget stuff when I go to talk to a doctor.