Why does Windows run CHKDSK on every boot?

Every time I turn on my PC, I get the following message:

Checking file system on E:
The type of the file systen is NTFS.
One of your disks need to be checked for consistency. You may cancel the disk check, but it is strongly recommended that you continue.
Windows will now check the disk.

CHKDSK is verifying files (stage 1 of 3)... 0 percent completed

I allow CHKDSK to to complete, but Windows does not load. This message appears every time I boot my computer.

Could someone explain me why this message appears and what I should do to make it disappear?

Solution 1:

When you schedule a check disk, an entry is added to the registry - for some reason, it's not being cleared.

1. Run the Registry Editor (Click Start, Run and type regedit then press OK).
2. Locate HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager
3. Change the BootExecute entry from:
   autocheck autochk * /r\DosDevice\C:
   to:
   autocheck autochk *

Source: http://support.microsoft.com/kb/158675

Solution 2:

If you have not asked for a chkdsk to be carried out, the autocheck will be carried out if the disk's "dirty bit" is set. This will be set if Windows is not shut down correctly, file changes have not completed or the disk is corrupted. It may indicate the disk is about to fail. For an external disk, it may indicate it was removed without using the 'safely remove hardware' function.

The fsutil command can be used to check the status of the dirty bit. Open a command prompt with admin rights and type:

fsutil dirty query D:

(Replace D: with the letter of the drive you are having issues with.)

Solution 3:

1. Click on your start menu and open the run dialog.
2. Type cmd and return
3. Next type fsutil dirty query D: (replace D: with your drive letter)

If the return message indicates that the volume is dirty then continue with these steps:

5. Next type chkdsk D: /f /x
6. After that finshes repeat step 3 to determine if dirty bit has been removed.
7. If it is no longer dirty then reboot and you should notice no more chkdisk.

Source of Information