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Exactly the same thing happened to me, and I've read about myriad others online who've had the same experience. I'm pretty sure I know what causes it, it's an intolerance to the proteins in the milk, which I didn't realise I had. There's both casein and of course the whey protein the kefir makes. Like you I was going really well on kefir for a while, and then bang, stomach pain and terrible diarrhoea. Some research I did confirmed that it's a classic sign of milk protein intolerance, and also in my case confirmed by a couple of realty bad cases of constipation as well, once with kefir and always when I eat a lot of Greek yoghurt (which is very high in milk protein).
Apparently you can re-balance the gut to make it tolerant of these proteins, so that has to be done first before you go back to milk kefir. You can also make kefir from non-dairy milks in the meantime, although for nut milks just need to be aware that nuts can be irritating to people with guts out of balance.
Also things started to go bad with kefir for me after I'd made a couple of really strong batches, with strong separation of curds and whey. Not sure if that was your experience or history too, and it may just have been coincidental for me, the gut reaction may have been on its way to happening anyway.
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