It's always easier to help if you describe what are you doing in detail. I use an earlier version of Pro Baking (4th, I think) and have never had a problem. Do you weigh ingredients? Or measure? My standard formula for biscuits includes 35% fat and 65% buttermilk. Other ingredient include 6% baking powder, 0.5% soda, and 1.25% salt.
I would also like to suggest 1:1 butter/soy substitutions. Lard is a good one, coconut oil, palm oil as these have less negative side effects in the body as hydrogenated anything. I would also recommend mashed banana or apple sauce for quick bread, cookie "butter" substitutions. That is if you can have any of these but I hope that this helps open the door for other experiments with your baking.
I am in the same boat as you guys with my own health....no soy, dairy, nuts, gluten, grains, eggs, nightshades, etc. for a while at least until my body rights itself.
Congratulations on your new addition to your family and wish the best in health and vitality through good eats and great treats!