Have you noticed a connection to what you eat and your pooping out fats? I mean, it may be that you don't tolerate certain kinds of fats. Maybe nut fats and olive oil are okay, but red meat and dairy is not.
Here's a weird one for you. I have gotten to where I can't do milk anymore. With or without acidophilus, no matter the fat content--it gives me gas cramps. But I can eat ice cream (and not the diet kind either!), sour cream, yogurt and cheese everyday with impunity. Don't EVEN ask me to explain that one!
only thing I can think of is that the milk is processed differently/less than the sour cream, yogurt etc- plus they usually have good bacteria in them... but that is strange.