I have been having a similar problem for years now , starting with my first few bouts of pouchitis immediately after take down 5 years ago. I have been struggling with both "stop" and "go" since the beginning and am on a bunch of meds, including Cipro which I have to take every day. I have a lot of other problems which have me and my docs considering whether to ditch the j-pouch altogether -- but those are not likely relevant to your question.
I didn't see any other posts from you, so if you've had a pouch since 2007 I am assuming been doing pretty well? Should we also assume you already know the impact of your diet on your pouch, along with the impact of balancing intake of solids and liquids? Given that, have you tried grape juice and GasX? Are you experiencing any abdominal pain which could be a sign of blockage?
Experience has taught me that sometimes my seeming unrelated problems are, in fact, related. It could be the antibiotics causing the back-up... Or could it be that what's causing you to suddenly have pouchitis is causing the stoppage? Your post was several days ago -- how are you doing now?
Hoping you are doing better! --Jennifer