I was thinking along the opposite line of Melanie. Can you stop the ginger biscuits for 7-10 days and see if the swollen eyes go away? If they do, then instead of re-introducing soy through a ginger biscuit, which may have other things in it that she's not had before and is reacting to (ginger? cinammon? possibly made or baked with butter?) re-introduce soy through something that you can easily be sure that it is the soy. Like.....say, tofu? Or edamame? Soy yogurt, soy margarine, even bread made with soy flour?
If the eyes don't go away after 7-10 days off of the soy then I would be more inclined to think that it is a hayfever allergy, but at the same time, swollen eyes from hayfever tend to get better and worse over the course of a day/week, not stay constant.
Anyway she doesn't seem to have any other symptoms (perhaps more grumpy than usual but not sure). I don't know whether she's just getting used to having soy and they'll go away.
The problem with this is that if she IS having an allergic reaction to the soy, being that it is such a highly allergenic food, I don't think it is a good idea to risk continual exposure to it. The immune system reaction can get stronger and stronger when exposed to the allergen, and it's not wise to continue giving a food that she is showing allergic reaction to. If it's suspected that the swelling is from the soy, I think you are best leaving the soy out for a while and re-trying again in a bit.
