I completed Yume Nikki these days... It's quite touching. Somewhere I read that Madotsuki is the poster girl for the tormented souls of our world. I tend to agree. There are lots of "Madotsukis" living among us, and during my life, I got to know two of them quite intimately. :)
However, as for what is going on in Madotsuki's head, I think that contrary to most theories, the question is not "what happened to Madotsuki", but rather "what did she do?!"
All this gore makes me think that she either did some very grave deeds (murder, even), or she is feeling genuinely at fault for something equally horrible.
Think of where you found the knife. Between two handprints, as if a person (Madotsuki) was crouching over it - in horror, guilt or both.
Also, the normal toriningen seem to be rather nice until you stab them. After seeing the room with the beds and the toriningen party, I have the impression that they may be teachers of some sort, possibly from Madotsuki's past, when "the event" happened.
(Though of course, as in real dreams, there are obviously various thoughts and trauma mixed in, like freudian fears, mother issues, etc.)