Several years ago I had a course of 30 days with Flagyl only (3x 400 mg per day, no Cipro) against chronic pouchitis and a treatment with probiotics (VSL#3) afterwards. For me Flagyl alone didn't have the same good effect as the combination with Cipro.
So if you have side effects I would contact your doctor and change something about the rather high dose of Flagyl, or perhaps alternate with another antibiotic or a probiotic.