Hi, I know with Nutramigen and Neocate it is best to slowly add it to their bottles. I know when I first started giving it to my son, Neocate, the first day or two he had really liquid diapers. I freaked, thinking he was having a bad reaction. His body got use to it and after a week his bowel movements were back to normal. Nutramigen is the same as Neocate, both amino-acid based hypoallergenic formula.
This is from the Enfamil website::
"stool consistency and color will likely be different when your baby begins using Nutramigen AA LIPIL, and this is normal. Anytime you change formula you may notice a change to the number, color and/or consistency of stools. If your baby is doing well on the formula, this probably is not a reason for concern."
Hope this helps. I'd just give it some more time for your baby to get use to the new formula.