OK, sorry this is so long, but we're right in the middle of this and wanted to share what has helped so far...
We have had similar problems with our little Jon Jon who is almost 9 -- he has had chronic diarrhea throughout his life, and they seem to go hand in hand with his seizures. When he is in seizure remission, he usually is also in diarrhea remission.
In the month of November, he had diarrhea or loose stool almost every day the entire month. And...like you mentioned, quite fatty.
It sounds like you probably have a malabsorbtion issue of some sort, and maybe gallbladder or pancreas issue? I'm assuming you're working with a GI doc?
We are currently (in past 2 weeks) working with both a GI doc and a Pediatrician who specializes in nutrition. Quite frankly, the Pediatrician/nutritionist has been more helpful than the GI doc so far. She prescribed a high dose of zinc, and also put him on Pancreatin (pancreatic enzymes) and probiotics. She also has him on MCT oil, which is absorbed more easily than other types of fats.
The zinc and enzymes seemed to do the trick in clearing up the diarrhea, but we had to cut the zinc dose in half (she prescribed 150 mg a day in 2 75 mg doses, which is super high) because it seemed to be triggering nighttime seizures. We started out on 75 mg a day, and then gradually worked up, and when he was on the lower dose, he didn't have seizures, but the higher dose did seem to cause some seizures. I researched this and found that zinc can both inhibit seizures but also trigger them (2 different actions on the brain).
The first dose of probiotic he got triggered 3 seizures, so we held off on giving him any more until he was 24 hours seizure free (which meant figuring out what was causing the nighttime seizures, and we think it was the high zinc dose, so we cut that out last night, and he didn't have a nighttime seizure). So...we gave him a second probiotic dose this morning, and so far, so good. He's supposed to get 2 capsules a day -- one before breakfast and one before supper, but we're going to just give the morning one for 3 days, and if he tolerates that, will give him the supper one.
I know you mentioned that probiotics seem to help a little. We had given him probiotics before, but they were the freezedried ones. Didn't seem to help at all. This time, we're giving him the live bacteria. I think the probiotic may have triggered the seizures because of yeast and "bad" bacteria die-off. I tried to find some scholarly research on this, and didn't, but lots of the nutrition sites talk about some side effects from the initial die-off.
I keep a food log and compare to diarrhea (and seizures), and I did note that regular yogurt seems to cause loose stool. Perhaps it's because the high amount of lactose that's still in the store-bought yogurt. Have you checked out the "Specific Carbohydrate Diet"? It recommends making homemade yogurt and letting it ferment for 24 hours -- so the bacteria can eat up all the lactose.
When Jonathan was on the Ketogenic diet for seizures, he did have one year of remission from both diarrhea/loose stool and also from seizures. In researching some of the possible reasons for this, I noted some strong correlations between the Ketogenic diet and the "Specific Carbohydrate Diet" (which is recommended for people with Inflammed Bowel Disease). For one thing, both diets cut out ALL grains -- not just gluten, and also sugar. Also, both diets eliminate most dairy products except for hard cheeses and butter -- which are low in lactose (the Ketogenic diet permits heavy whipping cream, which is also low in lactose). Apparently, the bad bacteria in the gut feed off of the sugars (which can be found in grains, sugars, fruit high in sugar, and milk sugar) -- so if the sugars are eliminated, or greatly reduced, the bacteria are starved.
So...as I mentioned, the Ketogenic diet bought us a year of both seizure freedom and diarrhea freedom. However, last March, Jon had a bad stomach virus, and while the rest of the family recovered in 2 or 3 days, he was still quite ill after 2 weeks. And ever since then he has had trouble again with both diarrhea and seizures, and in recent months, both got very bad. And then, he got another stomach virus several weeks ago, that made things even worse -- to the point that he had to be admitted to the hospital.
His Pediatrician/Nutritionist believes that what happened in March was that the viral illness created an inflammation which caused the intestines to produce more mucus than normal, and this mucus build up in the intestines is causing the food to pass through the gut too fast, and not get absorbed. So, her course of treatment is meant to help with the mucus buildup and improve his immune system and improve absorbtion. (In the meantime, the GI doc is doing stuff like checking for parasites and bacteria in the stool, and he also has an Ultrasound scheduled for this Wed).
Since his most recent viral illness several weeks ago, we have had him on only a few foods:
1) Carrots (good for gut inflammation, easy to digest)
2) Chicken (boiled, just small amounts)
3) MCT oil (4 grams per meal)
4) Olive oil (also good for gut inflammation, but too much can cause more diarrhea)
We have kept him on the Ketogenic diet, but lowered the ratio, so he is getting less fat and more carbs.
After about 1 week on this diet, we added in heavy whipping cream (he needs a lot of fat with the Keto diet) and yogurt. He tolerated the cream, but not the yogurt. After about 2 days on this regime, we finally saw some fairly normal bowel movements (but still pretty light in color). After several days, we added in green beans, well cooked. It didn't seem to cause diarrhea, but he also didn't seem to be digesting them (recognizable on the other end). We then added in apple (peeled and cooked), and that seemed ok.
So..this is what we're doing right now...gradually adding in one food at a time, waiting about 2 days to see what happens, and then adding in another. Something like you do with introducing solid foods to a baby.
When Jonathan was in remission, he ate quite a few veggies (raw and cooked)) and and some fruit, but only fruit low in sugar (like berries, star fruit, and melon). This is supposed to be good for gut health BUT when you are having diarrhea, should not eat any raw veggies until the symptoms are gone for some time.