I've had my jpouch for the past 15 years and I've had pouchitis, too, for all of those 15 years.
I've been on antibiotics (Cipro & Augmentin, plus 5 imodium) the whole time and I've always had good results with them, rotating in 2 days of Flagyl when things started to go awry (gas, bloating, stool begins to smell, increase in frequency)...which was usually after 3 weeks. Once I tamed the pouchitis with Flagyl, I'd go back to just Cipro/Augmentin/imodium and life was great. Over the past 1.5 years, however, I've noticed the daily antibiotic combo efficacy has waned...only lasting 10 days at best before I have to add in the Flagyl.
Within the past year, I've been having a harder time taking Flagyl. It's chalky and tastes nasty and I get nauseated even thinking about taking it. How do people take Flagyl without gagging? Is it possible to wrap it in something and swallow it, similar to how we put meds in hamburger meat for dogs?