While you're sorting out the possible food allergies, I'm sure you're investigating alt sources of calcium but over the years I've found ways to sneak it into my kids diets since we use milk in our diet but not as the "most important" source of calcium, especially since the casein is so very hard to digest for humans since it's for baby calves that are going to be hundreds of pounds someday.
Raw organcic sesame seeds ground up(designate a coffee grinder if you can) and sprinkled into foods like oatmeal,etc. Almonds are very high also, so maybe try some almond milk at the healthfood stores, I made some but it was kind of labor intensive and messy. Tahini(?) is sesame seed butter(like peanut butter) and they make almond butter, both are great sources of calcium. Maple syrup is naturally high in calcium, even more than milk, ounce for ounce. Goes great with oatmeal.
I found with my 17 month old twins that they could only eat very yellow bananas, not freckled or else a terrible yeast diaper rash. I also added powdered acidophillus to counter the yeast issue and try and build up healthy gut flora. I can put a few raisins out for help in the BM department. Also canned pears, I get the halves and slice it into 3 or 4 little sticks dry it off with a paper towel and my toddlers pick them up and feed themselves. That works great for keeping them regular if they need a little boost.
I have tried some of the juices with added calcium, my kids didn't like the oj but there's a fruit punch by Mott's I think that they like. Also, Total cereal has a lot of calcium added to it.
I hope you can get the help you need, it seems like you've had a lot of good advice already. Trust your instincts.
LaurieK
www.mymonavie.com/LaurieK