There is one other option you might want to consider before entering "the lion's den" of the adminstration office. Your school should have counseller's available for the students. I know that it has been many (many) years since I was in high school in Canada, but the counsellers at that school helped to straighten out "paper problems" like this...

I also hate to be the one to tell you this, but the paper trail doesn't get any better at university. After being in school for over twelve years and at many different universities, they are all the same. You may not like the paper work, but for the sake of your sanity (and graduation) you will learn to deal with it