Leakage and nighttime incontinence are definitely signs of flaring or poorly controlled pouchitis. Chronic refractory pouchitis can be confirmed by pouchoscopy. I had about 25 consecutive annual scopes that showed it before Remicade eventually dialed back the pouch inflammation.
Like Scott I would be way more suspicious of pouchitis than a "food intolerance". And if the pouchitis doesn't get treated on the belief that something else is going on, it will get worse. Unfortunately this is the road many people go down with pouchitis, where it becomes very serious before anyone gets their head wrapped around what's really going on. It's sort of like the gastrointestinal equivalent of a rip tide. You do not want to get caught in one and if you are, you have to recognize what you are in.