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Check Disk - Disk Checking Runs Upon Boot

Check Disk runs on every boot: Note - I have seen this happen when Windows File Protection has either been disabled or not allowed to run upon canceling the bootup Check Disk.

Suggestions and Checkpoints:

Go to Start/Run/CMD and type in: fsutil dirty query c:
(Modify the drive letter accordingly)

If it comes back as dirty, it hasn't cleared. For more information go to Start/Run/CMD and type in: CHKNTFS /?

Option: From a command prompt type chkntfs /D and then reboot, a chkdsk should run but not again on next boot.

This edit does not work for all users, circumstances depending:

Disable or Enable CheckDisk Upon Boot (Line 82)
http://www.kellys-korner-xp.com/xp_tweaks.htm

To use the Regedit: Save the REG File to your hard disk. Double click it and answer yes to the import prompt. REG files can be viewed in Notepad by right clicking on the file and selecting Edit.

Chkdsk Runs Each Time That You Start Computer
http://support.microsoft.com/support/kb/articles/q316/5/06.asp

Checkpoint:

Go to Start/Run/Regedit and navigate to this key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon

Highlight the Winlogon file.

In the list look for "SFCScan", this should be set to (0) if it is set to (1) the scan will happen at every boot.

Go to Start/Run/Regedit and navigate to this key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager

Look for the REG_MULTI_SZ value with the following name: BootExecute. This value contains commands that will be executed at startup. The default value is: autocheck autochk *

After scheduling one or more chkdsks, the entry will contain one or more autochk lines. Delete each of these lines and put the default one in place.

If you always want a check to be performed at startup, change the value to: autocheck autochk /f *

If you don't want any checks to be performed, delete all autocheck entries.

Last checkpoint: Modify as needed:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\MyComputer\cleanuppath
Registry entry should read: %SystemRoot%\system32\cleanmgr.exe /D %c

How to schedule a CHKDSK on every boot
Chkdsk Runs Each Time That You Start Computer After Upgrade to Windows XP

Scandisk after a Bad Shutdown - Go to Start/Run/CMD and type in: CHKNTFS/T:4
Where 4 is the amount of waiting time.

Automating Disk Cleanup Tool in Windows
An Explanation of CHKDSK and the New /C and /I Switches

Use the scheduler and run chkdsk with the automatic switches for unattended operation (chkdsk /? will list the options for you). To open Scheduled Tasks, click Start, click All Programs, point to Accessories, point to System Tools, and then click Scheduled Tasks. You can also use TweakUI to automatically login if you have logged off the system to allow chkdsk access.

Restore Disk Cleanup - cleanmgr (Line 84)
http://www.kellys-korner-xp.com/xp_tweaks.htm

Disk Cleanup freezes during the Compressed File Phase: This edit correct the problem:

Disk Cleanup - Compressed Old Files Freezes (Line 48)
http://www.kellys-korner-xp.com/xp_tweaks.htm

To use the Regedit: Save the REG File to your hard disk. Double click it and answer yes to the import prompt. REG files can be viewed in Notepad by right clicking on the file and selecting Edit.

How to Automate the Disk Cleanup Tool in Windows XP
http://support.microsoft.com/default.aspx?scid=kb;EN-US;Q315246