I also have lots of space missing. Pagefile.sys is 1,681,308KB and hiberfil.sys is 1,260,980KB. I have run the HijackThis. The notepad came up. Do I understand correct by reading that I must not press the "fix checked" button?
Those are both legitimate windows file that will take up alot of space. You need the pagefile unless you are on an SSD to be a backup incase you run out of ram and Hiberfil.sys if the stored data from your last hibernation.