I know how vitamin b12 deficiency can affect the organism, I also had to take B12 some years ago, took a long time until the deficiency was diagnosed. My little nephew is suffering form ADHD and he has to take Ritalin pills and you can really see a big difference in his behavior depending on the Ritalin. You can easily notice when the Ritalin loses its effect and he starts to get nervous and bumpy. It's really tough when you're well-being is so highly related to a certain medication.
Yes, soy intolerance can be a reason, I have a friend who has problems with it. If he eats or drinks soy (accidentally), then he can't sleep at night and his stomach aches. First, even the docs didn't know what the problem was but then they discovered the intolerance. The most important thing is to find out the cause for the problems, food intolerances are often difficult to discover.