I don't think that it is lactose intolerance. I don't drink milk at all, and I have no trouble with yogurt whatsoever. Acidopholis probiotics don't give me any trouble, but they aren't all that effective. I never have trouble with fermented foods like sauerkraut and kimchi. I buy them whenever I can but I'm a total failure at making them myself. It is Kefir and the high-end probiotics (Dr. Ohira's for example) that I have trouble with.
I tried water kefir grains and had the same trouble. I make kombucha and that works well as far as digestion goes, but I can only tolerate kombucha in small amounts as the kombucha stirs up the mercury stored in my body. (I know you don't believe much in mercury toxicity but it's for real, I promise.)