I recently began taking probiotics and including them in my diet -- through supplements, regular yogurt and Activia. I had the same response as Eve8 and started getting a slight heartburn. I just figured it was a "Herxheimer Reaction" also known as the healing response -- sometimes symptoms get worse before they get better. I've persisted with the yogurt and the probiotics and not only is the heartburn gone, but I feel healthier every day.
My take on it is that the good bacteria in the yogurt "fight" with the bad bacteria and move them on out. That causes some reflux. But if you stay at it, the good guys will win.
BTW, I would NEVER (unless I was about to die) take an antibiotic again. That stuff will kill you. Better to take the natural pro-biotics so that they do the job on a daily basis and you never get to the point that you need the antibiotics. Just a thought. Good luck to you.