I can take a look at the save file if you like, see if I can figure out what's going on. I would think you'd remember chapter 4 if you'd played it, it's fairly dramatic! There's details of how to send the save in the readme file,
Oh yea, there's one other little oddity that I found. During Avenging Angel, after the whole isolation thing, you have to publicly "apologize" to your teacher in the morning at school. Well you can completely get out of that morning punishment by making Missy late to school. ;-) I wanted to see if something even worse would happen if Missy was also late, but it just treats it like she apologized, and lets her off the hook entirely.