It could be just the fact that you are introducing 'foreign' organism into the digestive track. Foreign as in to the current residents.

Lot of differences in probiotic supplements. So maybe now you stumbled into something that works for you? I would say keep it up if your bowel movements have improved. Things will probably settle down in time. For clear skin you absolutely need good bowel function.

It could be die-off symptoms, though I can't be certain. If you read the GAPS website, it references to the probiotic and working up to a therapeutic dose. You will get to a dose where you experience die-off symptoms, you stay at that dose until they dissipate, then slowly increase the dose.

http://gapsdiet.com/Bio-Kult_Probiotic.html this is the page I'm speaking about

I have no experience thus far with GAPS/Bio-kult (though I just contacted a local GAPS practitioner) so I can't say what the die-off symptoms are, but the sensations you describe in the stomach very well may be die-off symptoms.

Hope this helps.

My naturopath recently put me on a high dose of probiotics to increase the good bacteria in my gut (the levels were shocking). I immediately experienced symptoms similar to the one's you've described which included: stomach cramping, nausea, bloating and just a yucky feeling in my stomach. He's been seeing me for a while now and that reaction helped him diagnose me with SIBO (small intestinal bacteria overgrowth) and he told me to stop the probiotics immediately as they were only making the problem worse (feeding the bacteria in my small intestine and inducing the symptoms). And I'm now on a natural antibiotic to get rid of the overgrowth of bacteria. Once we have cleared it effectively I will go back onto the probiotic regime and hopefully get my levels of bacteria back to a healthy balance.