I can't help much on the possible diagnosis, as I'm going through similar with my own DD & so far getting nowhere, though thats not been helped by our GP diagnosing IBS & refusing a hospital referral as she reckoned it would just get reffered back to her for management that is until I went back recently as its out of control & told her I was booked for a second opinion but needed some sort of short term help as DD has been VERY ill with it lately & missing a lot of School again, getting sent home etc.
I do know with my own DD that she is very chemical sensitive, & any artificial sweetners, certain preservatives (benzoate ones) & colours set off bad flare ups, as does stress.....last ongoing problems we had turned out to be caused by problems at School with a very disruptive out of control child in her class, who she feared & hated, but sadly the child had "a soft spot for her" & wouldn't let her be....so in the short term that might be worth talking to your DS about.
We are finding with DD, that everytime she needs antibiotics, her problems esculate, & shes now also wheat & dairy intolerant, she could before eat cheese ok, but not drink milk, but now its everything, but she can usually drink lactose free milk....... so I've been giving her the Viridian synbiotic Childrens stomach flora powder, which have helped a bit, but not enough, but are good to give her regardless
I've no answers, but I have had a bit of a breakthrough, in that her School nurse suggested a bland roughage free diet for a few days, & I was already looking at a macrobiotic type elimination diet avoiding all possible irritants, such as those above, & the nightshade family of veg, which includes potatoes & peppers........
so I've taken the roughage free diet a step further, & since yesterday I've given her nothing but fish & white rice,....the fish will have omega oils, which are need amongst other things for gut health......also with a bit of low salt over it, as it contains sodium & pottasium, as she is losing so much fluid she needs rehydration salts,........
I've also cooked the rice with Tumeric, which is a spice that is also used as a stomach medicine in India etc, it has little flavour of its own so DD is happy to eat it.........even the Buscopan our GP give her this week did not stop the diareah & cramps, but touch wood, the above has
its the first full nights sleep we've had in weeks, & no diarreah at all since yesterday morning when she was again ill at School , & though her tummy is still very tender, the cramps seem to have stopped too
I know this isn't a cure, as like you this has been ongoing with flare-ups & we;ve only just now got a hospital referral, but at least it seems to be working to give her a break & help her stomach settle down again, so might be worth trying with your DS?