Create a file, C:\Y.TXT that contains: Y
Create a file C:\CHKBOOT.BAT that contains:
chkdsk C: /F <c:\y.txt or chkdsk C: /F /R <c:\y.txt
If you have a D drive, just add another line, etc..
If you always logon to the server, just put C:\CHKBOOT.BAT in your StartUp group or download AUTOEXNT. This service will execute a batch file during system boot.
You can do this with one file as follows: (Provided by Keith Gorham)
echo y | chkdsk Drive: /f