When I made water kefir I don't recall having that problem but it did help with bowel movements.
Yes, it is doing wonderful things for you and I would think that once you get adjusted to it that "poot and run" syndrome might end too :::wink wink::: but I can't say for sure cause I just don't know for sure.
Poot away girlfriend and know your body is lovin' you for it lol,