That would be my assumption. Usually when you start replacing one thing with another, of an issue arrises it's the "new" product. Also, soy and dairy have some similar properties. Many people who can't tolerate soy/dairy can't do the other.
If she's not having other issues (mainly GI) it would be classified as an intolerance over an allergy.
A 2 week trial may not be long enough to really tell. I would try a bit longer (but it looks like you may have already started it). Also, there are many people who can eat yogurt and some hard cheeses but not other forms of dairy.
It has been longer than 2 weeks, but since I noticed a difference almost immediately, I was pretty sure we found the culprit. The point of adding things back in now is to see what she can eat. She'll only have yogurt for dairy for a few days.
We are using Fleischman's light margarine. We don't eat alot of soy and I quit using margarine years ago. I bake with butter and cook with olive or canola oil. But, this week I made bread using margarine and she used it on pancakes and baked potatoes. I am thinking that since she isn't allergic (only issues are gi-related), butter will be fine in moderation, as long as I use rice milk or almond milk in cooking. We are also at the point of challenging the intolerance. I'm starting with yogurt today.
This may seem pedantic and painfully obvious, but is Fleischman's dairy-free now? It used to be that Nucoa was the only mainstream brand to not add whey or another dairy derivative to the recipe.
I might hold off on the butter until you can challenge the other dairy. Yes, if it is an intolerance she should be able to digest butter better than some other dairy forms.
"Let me see you stripped down to the bone. Let me hear you speaking just for me."