Here is what the GI doctor told me.
Most of the nutrients from the Neocate are absorbed in the small intestines, so the nutrients never hit the large intestines (which is what produces waste). Normally when food gets to your large intestines, your gall bladder produces bile to breakdown the food. Since Neocate bascially does not need to be broken down, the bile comes out in the poop. That is why it is dark green and smelly, but NORMAL....
This also makes perfect since why an intolerance reaction does not normally happen until 1 to 2 hours after you have eaten because that is when it would hit your large intestines when your system is trying to break down the food.