Are you still making the raw goat milk formula? Is it the homemade recipe that is on the Weston A. Price Foundation web site? Maybe try the liver-based formula?
Also test for food sensitivities /allergies. This might sound crazy, but I was reading about it on the mothering.com forums in a really long "elimination diet" thread and they were swearing by using a pendulum as a way to muscle test for that. This is the thread here, although its mainly women that are breastfeeding, I think it would still be applicable because the mother's test on themselves and its usually the baby is reacting to the same foods:
I would test the cod liver oil and any other solids the baby is eating, just to be sure. I tested a bunch of foods lately and I think I may have found a major culprit. It says no chicken, eggs or turkey for me.
What brand probiotics? Natren is a good brand. The "Life Start" is not dairy free. But "Healthy Trinity" is dairy free.