Could it be a food intolerance? I struggled with digestive issues for years (still do, on occasion; it's clearly just my lot in life) and tried every probiotic, prebiotic, digestive enzyme, bitter, whatever the fuck and nothing solved the issues completely until I actually did an elimination diet and found out what my trigger foods were.
And your trigger foods can be pretty much anything! Seriously, like a fairly obvious bodybuilder type diet could be something like:
breakfast - egg whites, couple of whole eggs and oats
meal 2 - chicken, rice, broccoli
meal 3 - whey protein shake with some carb powder
meal 4 - flank steak, potato, salad with tomatoes, peppers, onion
meal 5 - cottage cheese, peanut butter
Or whatever (don't anyone say that's a stupid diet because it's just an example). Those are all fairly reasonable bodybuilding meals, but every single one of those has a potential trigger.
In meal 1 - oats, egg whites and whole eggs are all known allergens
In meal 2 - some people have a really tough time digesting the insoluble fibre in broccoli (I really do - can't eat the stuff)
In meal 3 - whey protein is a very common allergen
In meal 4 - nightshades like tomatoes and peppers in the salad, plus onion is really high in FODMAPS which will fuck you up if you're sensitive
In meal 5 - the whey and casein in the cottage cheese is another potential allergen, and I'm sure you know how allergenic peanuts can be.
See my point? Lots of foods that are considered "clean" or "healthy" can actually be pretty rough on some people. I know through trial and error that I have to eat a low FODMAP diet and a diet low in insoluble fibre otherwise I'll be bloated all day and diarrheic (gross, I know, sorry) every morning. I also have to keep on top of using probiotics or, if I do have an issue, it'll last way longer than it otherwise would.
The real bitch is also that food allergies can develop over time! So you might have been drinking 2 whey shakes a day for the last 5 years with no issue then all of a sudden your body just rejects it.
It's one of the reasons that the carnivore diet is so popular among people with IBS or autoimmune disorders; for whatever reason no one ever seems to have an allergic diet to red meat. I'm sure someone who knows more about that could explain why but the people (some would say idiots) who subscribe to carnivore are really just doing an elimination diet without realising, but I digress...
Anyway, hope that helps and maybe gives you another angle to approach this from.