One easy way to determine if a drive letter is marked as dirty and will require auto chkkdsk on boot is to run the command fsutil dirty query C: in Command Prompt. If the fsutil tool reports that the drive letter is not dirty, the disk checking process will not want to run for that drive. However, when a drive letter is being marked as dirty, we discovered the location of the hex values on the drive that are being modified and resetting the dirty bit hex value to default will magically stop the auto disk check on boot.
While resetting the dirty bit manually would be the best solution for many situations, it is more difficult to do on system drives such as C because they will be locked and not allow editing from within Windows to change the bit value. Another option for these drives is to simply instruct Windows not to bother checking whether they have been marked as dirty on boot, so you’ll never get a request to auto check them again. Here’s how to disable or stop Check disk from scanning your drives in Windows boot for Windows XP, Vista, 7 and Windows 8.
There are people who suggest editing the registry to do this which works if done properly, but the recommended and safer way to disable auto Check disk from starting up is using the /x switch via the chkntfs command in Command Prompt. This switch will exclude a drive from the default boot time check. To get to the Command Prompt, go to:
Start -> Run (or Win key+R) -> type cmd and press enter
If you have drive C: as the drive you want exclude, then the command to disable chkdsk from scanning the C: drive would be:
chkntfs /x c:
If you have a second drive to exclude, C: and D: for example, you can disable Check disk with the command below. Simply add all the drives you want to exclude in this way, separating them with a space.
chkntfs /x c: d:
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