Because of the way that operating systems access files, only one program can access a file at once. If a file is being used by another program, or is a system file that is constantly used whilst the operating system is running then the virus scanner can't access it to fix it.
A boot time scan is a virus scan that is run before the operating system fully loads up. This means that the virus scanner can have access to all the files on the computer with no chance that they're being used by another program or the operating system.
This means it is much more likely to find and fix viruses that have affected critical system files, like the contents of the c:\windows folder on the windows operating system.
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