well not everyone will experience that, but yes carbs can begin to ferment (spoil actually) if they are bound up with a lot of more slowly digesting protein. Problem is you need the calories to grow, right, so you kinda have to suffer with it.
To answer your question though, if it's straight whey concentrate or isolate on an empty stomach, I'd think most of it would have moved on into your large intestine after about an hour and a half. Dont use cold water b/c that slows digestion down some.