Are you buying store bought or making your own? The reason I ask is because I used to buy store-bought SOY milk (didn't have a problem) and recently started making my own almond milk (and didn't have any digestive problems). So, it could be however the company makes it, if it's store bought, is not agreeing with you.
Another thing: when you move toward more "whole foods" you actually need less to feel satisfied. So, if you normally would use a cup of milk on ceral, for example, you may only need 1/2 cup for your body to be satisfied. Could be too much good stuff at one time if you traded it ounce for ounce. :D