I know it's been awhile since this subject had a post, but just wanted to share my same problem I had with my daughter, with an easy solution.
Since birth she had soft stools that would ooze out normal diapers and it continued, I could only use diapers with elastic around the legs. Like others here, her weight gain and health and everything else was perfectly normal so her doctor said to not worry about it. I gave her a lot of apples and bananas, as well as juices, which were supposed to help harden up stools, with minimal help. Around age 2-1/2 years though, she started waking up in the middle of the night vomiting. Every night.
While at the doctor about the vomiting, we started thinking about possible food allergies. And the only thing she had consistently on a daily basis (she was in pre-school, so had a good varied diet) was milk.
I stopped the milk and all dairy products, and the vomiting instantly stopped that first night... and so did the soft stools she had all her life. She apparently was somewhat lactose intolerant at birth, which just became progressively worse by drinking milk daily, which eventually ended up with her vomiting nightly.
I'd try eliminating all dairy products for awhile and see what happens. And don't do what I did the first day... skipped the milk but brought home a cheese pizza... wasn't thinking all dairy products at that point yet.