These instructions are step by step for Windows 98. They are similar for other Microsoft OS's but not step by step.
To add ScanDisk to your StartUp folder
On the taskbar, right-click Start, and then click Open.
Click the Programs folder, and then click the StartUp folder.
On the File menu, point to New, and then click Shortcut.
In Command line, type:
scandskw.exe
Click Next.
In Select a name for the shortcut, type:
ScanDisk
Click Finish.
To check for disk errors when your computer starts
In your StartUp folder, right-click ScanDisk.
Click Properties.
On the Shortcut tab, type one or more of the following after the text that appears in Target:Type To
x:
(substitute the drive letter for x)
Specify the drive you want to check.
/a Check all your local hard disks.
/n Start and quit ScanDisk automatically.
/p Prevent ScanDisk from correcting any errors it finds.
This should fix your problem
Good Luck!