How to repair damaged start up files?

Sometimes when I run Scan Disk, it says I have a damaged start up file that reports erroneous available disk space, but that it has repaired the file. Microsoft System Information says I have 337 MB of available space of 4102 MB(Fat32), but when I try to download a 150 MB file it says I do not have enough disk space. How do files get damaged? Is there a way to repair damaged start up files