What else are in the cookies? Any other foods you're eating that could be upsetting? Nightshades (tomatoes, potatoes, peppers, etc.), onions, garlic, spicy stuff, cruciferous veggies? I'm finding out my DS is sensitive to things I never suspected now that we finally have enough of the things out of his diet that was bothering him.
I empathize... it is super hard to figure it out. Are you keeping a detailed food journal with every food you eat, ingredients and her symptoms? That will probably be the key to figuring it all out... for DS the reactions sometimes don't start until 2-4 days after he has eaten the food. Basically, whenever the poop comes out is when we see the reaction (his are mostly rash oriented.) The delay makes it even more difficult!
I found for DD1 that certain things she would tolerate at first and after a couple days she would begin reacting to them. Also, my allergists told me that the window for reaction is 4 days!
Becky- Wife to DH, Mama to "Nani" (July '08) "Coco" (July '10) and expecting one very wiggly baby boy in May 2013!