Hello, 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?
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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.