Confirmation bias can be a strong thing. And it affects us all. I'd suggest you rexamine to be sure that it or a similar cognitive bias is not at play, particularly given the wording you used above which is very suggestive of putting yourself in an ideal situation where such biases can work:

>we sometimes are able to sort out ingredients after the fact, and if she has the reaction, it will show up if we look deep enough.

Not saying she doesn't have an issue with gluten (I don't know you two so how the heck would I know?) but given she has symptoms of something you owe it to yourself to make sure you are addressing the correct root cause.

EDIT: looks like cpncrunch's sibling comment is getting at the same thing, only I would not use the term "placebo" for what could be at play here.