Are you taking probiotics? Sometimes there is an "adjustment period" when you take antibiotics, because they essentially kill everything in the gut, even the good stuff. It can take a few days to a few weeks for the gut to normalize after taking antibiotics. It's actually one of the reasons I hate taking them, because they do screw up my system for a few weeks. Basically, though, I wouldn't jump right back on the cipro just yet. I'd actually try starting probiotics to see if you can get some good flora going; hopefully that helps. However, if the pouchitis-like symptoms persist, worsen, or clear up then return, you may need to speak to your GI and try a course of cipro and flagyl next time.

I too just came off antibiotics and also Endocort. I had such bad Big D for 4 days. It was literally coming out of me. I had also ran out of antibiotics and was waiting for my online pharmacy to deliver. So, I literally loaded myself up with every probiotic I had in the house and doubled and tripled the dose, plus I added kefir. In a day I was in good shape and been getting better every day. My surgeon told me today to rotate probiotics every 3 weeks.