Maybe it's because soy is poisionous before it's processed.
I'm also a nurse and think it's related to gm soy exposure and cross sensitivity. I don't think they'd want to admit that gm soy is responsible though.
My goodness, people have been eating soy since the beginning of time. You sure you've got the right bean? Soy is made up of about 50% oil, 35% protein and the rest is a combo of carbs and minerals. Once the oil is pressed out of the bean, the remainder (cake) is used mainly for animal feed. If humans eat the cake before it's processed, the carbs left over cannot be be metabolized in the gut and transfer to the large intestine. Here, when microorganisms get a hold of it, a lot of gas can be produced. This is a good reason not to feed your dog any food made with unprocessed soy.
Other than this there is absolutely nothing wrong with soy beans. Are you sure you're not thinking of castor beans?