OMG, I was just coming here to post this exact same question! How weird is that!
I've been taking Carlson's fish oil capsules since before the start of the pregnancy. I'm now BF and dd is about 12 weeks old. I've eliminated dairy and soy. Today I took my fish oil in the morning, instead of last night like usual, and starting late morning it's all diahrrea and mucus. But her first morning poop, which was before I had the fish oil, was more normal - actually seedy and much thicker than it's been for weeks. Hmmm...
(but I also put egg white protein powder into my oatmeal this morning... could be egg too - boo hoo)
I'm going to skip fish oil for a week and see what happens. If it turns out to be the culprit (keep your fingers crossed! I really miss milk. I'm not holding my breath though), I'll want to switch to another omega product. Is there anything made of, say, flax or something, that comes close to the potency of fish oil?
FWIW, I think Carlson's is an excellent brand, so I think that if there's a problem with Carlson's, then all fish oils are out.