The gut mucosa are crucial to building and maintaining the immune system, are they not, @Jonathan Edwards? Could this be one key to fluctuations, including full-blown remissions and relapses, at least for some people?
This looks a rather interesting paper on the gut and immunity.
A lot of antibody is produced in the gut wall by plasma cells that lodge there but I am not sure about events in the gut being that important. My impression is that the gut is permanently full of all sorts of dreadful stuff and has a pretty good way of coping. I suspect that gut disturbances occur when the immune system is activated because antibody production revs up there as part of the response - rather than the other way around.