Oh my god so I've always missed one gem, and I didn't know where to find it so I could get the gallery. So I looked it up and it's the one hidden in the West Passage and I nearly screamed b/c there's no way I would have been able to find that without the internet...
Miss Library is actually the clone of Aya. "Ogre" took Aya's father with him in his world. He missed his daughter so much, that he created a clone of her. If you try to name Miss Library "Aya" she will answer with "sorry, but only my father is allowed to call me that" In her room is a picture of Monika (Aya's mother) and a couple of dolls. you can also find her books and her bow. That Zombie scientist you see in Misao is actually Aya's father. There are also other hints, that proof that Miss Library is the clone of Aya, but this comment is already long enough^^'
Yes you're right, it's quite the same melody. I also think this is actually the main theme just a bit slower and "darker". If you know the game Misao, you maybe noticed that the theme of the library is the same as here. :)