I wonder if it's something in your diet. My younger son got extremely fussy if I had eaten broccoli (or anything in that cruciferous family) or orange juice or any fruit with a small seed like strawberries, etc. Also, some spices could well change the taste of your breast milk and aggravate her. You might try keeping a food diary for yourself and look for the pattern.
My older son had huge issues with reflux and gasiness and in hindsight, it was likely due to dairy in my diet as we later learned that we both have a dariy allergy. I had detected mine, but just thought it was lactose intolerance, so I had removed dairy before my younger son was born. That also might be why I had a much healthier pregnancy with son # 2.
Also, I can't recommend highly enough that you get some support from a local La Leche League group:
http://www.lalecheleague.org/resources/assistance.html?m=0,0
The local group in Lewisville provided me with invaluable support when I was struggling with breastfeeding my first son.