From what I've read, unfermented soy is what has been shown to cause some problems. The issues I have seen are higher estrogen levels, intestinal distress, and finally dementia. The only thing I've seen a real study on is actually the dementia part.
A study of Japanese men living in Hawaii was done, and those that ate tofu 2x a week or more had a statistically higher chance of dementia. Now in this study they really didn't survey a large sample population, and only stuck to japanese men. Here is a link:
http://www.ncbi.nlm.nih.gov/entrez/quer ... t=Abstract
I lived in China for 6 months, and a lot of the tofu that the Chinese consume is "stinky." They age it in pig pens for a month, so it develops these black moldy spots on it, and it smells like a toilet. They love it, I would almost vomit everytime I tried to eat it. The Japanese also have aged tofu as well, which is brown and pastey, and equally as appetizing. I so I wish I could get a taste for it though.