If you are keeping a food diary, it sounds like you may have your answer. The next step would to eliminate dairy in your diet for 3wks, then try a glass of milk again. If you are experiencing the same issue, then you for sure have your answer.
I don't give my 2yr old cow's milk, nor do I drink it as there are much better forms of calcium out there. We do a combination of rice and coconut milk. Rice milk is fortified with the same nutrients as cow's milk, so you do not have to worry about calcium intake. Getting enough vitamin d3 is the big concern as many of us (about 90%) are deficient. (If you bfeed, then bfed babies need 400iu daily) Changing to a dairy-free diet is not hard at all. I do prefer rice, hemp, coconut or almond milk over soy. So Delicious makes a wonderful line of coconut milks including yogurts, ice creams, coffee creamers and half gallon milks.
Have your vitamin d3 levels checked as your son's at his next appointment. Here is an article I wrote in my family health column about D3: http://www.examiner.com/x-7158-Chicago-Family-Health-Exam...
Happy, Healthy New Year!
J. W. MPH
Maternal and Child Health Educator
Chicago Family Health Examiner