I just started taking Apo Amoxi-Clav (antibiotic) this week for a root canal. Boo. When I first started taking it I was always on the run to the bathroom. A couple days in and it's eased off a bit. I told my doctor and she said that diarrhea was common and although but if the was any blood in the stool I needed to get a bacteria (c. difficil?) test done immediately. She even wrote out a requistion form and left it in my file so that I could just call the office and have the form sent to the lab super fast. I don't think you should stop taking them... That's dangerous with an antibiotic (so I'm told).
I'm also taking probiotics (when I remember!!) 2 hours after I take the antibiotic. I hope this info helps you.