Tony,
It is possible oral pharmaceutical probiotics cause problems in the small bowel but since them only offer temporary colonization, the problem will disapear by itself once you stop the intake. There is a big controversy about the role of probiotics to treat SIBO. I have written in this forum many times that some MDs think SIBO is a pathogenic overgrowth in the small bowel, and another group believes SIBO is an overgrowth in numbers not matter what kind of bacterias. Anyway, I think the best thing is to leave the body alone to find its balance and gives it good nutrition. I don't plan on taking more oral Probiotics. I have always thought Prebiotics are better, specially Lactulose. If I have to take Antibiotics in the future my own feces will be my probiotics when I finish the treatment. http://en.wikipedia.org/wiki/Fecal_bacteriotherapy