Sorry to hear you had such a bad reaction to your milk kefir [or veggies?].
I've been making it for a few years now [and water kefir & kombucha] and read a lot about it and have never heard of anything like this.
Do you use regular store bought milk every time? Or raw milk? Did you use another brand or some other kind of milk or a different fat percentage milk?
I hope someone will be able to give you a clue about what it might be. Keep researching on the kefir info sites in the meantime. I don't blame you for stopping drinking it at least for now.
Hope you get to feeling better and find some answers. I'm curious about this too!