I have been making goat milk kefir for a year now, and my mega flare-up occurred while I was consuming it. I almost am wondering if kefir is far too strong for my system... I really had a dis-taste for it for a while during my flare up - my body preferred yogurt so I made that instead - though kefir tastes good again now. However, I have not been eating it for a while (switched to goat milk for my smoothies) and my GI seems happier. I have read that both kefir and yogurt can contain too much histamine for some people, so it could be that or it could be something germain to the culture itself...
Kefir can contain up to 30 different cultures, it is fermented with bacterial & beneficial yeast colonies that look like little florets of cauliflower. They are symbiotic little 'creatures' that you transfer from one batch of milk to the next. They are pretty funky little beasties.
The longer it is cultured or the more kefir grains that are used to make it, the more acidic it becomes and the whey will separate out.
I have read that it can tend to be constipating if fermentation goes longer than 24 hours, and it can tend to cause diarrhea if it's fermented for only 12 hours or so. Since I tend toward IBS-C, I tried to use 12 hour ferments to help, but didn't find it very useful.
So while I'm still making kefir for the rest of my family (even my 88 y.o. grandma eats it daily), it gets a mixed review from me.