Have you had any problems with fermented foods, water kefir, or kombucha (assuming you've tried any of these)? It could be that your gut flora just needs to adjust to the good bacteria in kefir, or it could be that you are sensitive to a naturally occurring food chemical called amines...fermented foods are high in amines. I had 10 days of horrible diarrhea after drinking a few cups a day of water kefirs, and I eventually figured out that it was because I am sensitive to amines. It took a good week for my stomach to recover even after I'd entirely stopped the water kefirs, and it took a couple of weeks after that before I could tolerate fermented foods again. Then smaller amounts of fermented foods gave me bad gas (it took me a long time to figure out why)..qaA
Anyhow, you might want to wait for a bit to try kefir again. When you start it up again, try with small amounts (maybe even a couple of tablespoons a day at first). If you still have diarrhea from that, or if small amounts are okay but you get diarrhea when you try to drink larger amounts, I think there's a good chance that you are sensitive to amines.