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Know what to do when Check Disks malfunctions in Vista

The Check Disk application in Microsoft Windows Vista can sometimes malfunction, causing problems during the boot process. In answer to several TechRepublic member questions, Greg Shultz explores the problems and describes how to permanently fix them.
In the September 25, 2008, edition of the Windows Vista Report (How do I ... use the Vista Check Disk tool for hard disk analysis?) I showed you how run Vista's Check Disk tool in analysis mode. As I did, I mentioned that to run Check Disk in full repair mode, you select both the Automatically Fix File System Errors check box and the Scan For And Attempt Recovery Of Bad Sectors check box, as shown in Figure A, and click Start. When you do, the Check Disk GUI will schedule the DOS version to run at startup and prompt you to restart.

Figure A

To run Check Disk in full repair mode, select both check boxes and click Start.

Since that blog post ran, I've heard from several readers who have attempted to run Check Disk in full repair mode but have discovered that Check Disk fails to run at startup. I've also heard from several readers who have run Check Disk in full repair mode and have discovered that after doing so, Check Disk runs at every startup.

Fortunately, there are ways to work around both of these issues. In this edition of the Windows Vista Report, I'll show you what to do when Check Disks malfunctions in Vista.

This blog post is also available in PDF format in a TechRepublic download.

Check Disk fails to run

When Check Disk fails to run at startup, the cause is typically a configuration error or a slight corruption problem in the registry. When the Check Disk GUI schedules the DOS version to run at startup, it actually makes a change in the registry that triggers the Check Disk operation to run as the system starts up. If that entry isn't configured properly due to some glitch in the system or if it becomes corrupted by a third-party utility, Check Disk will not run at startup.

To fix the problem requires that you modify the registry. Since editing the registry can be a dangerous operation, it is important that you back it up before you begin.

To launch the Registry Editor, press [Windows]+R to open the Run dialog box. Then type regedit.exe in the Open text box and click OK. You'll then encounter a UAC and will need to respond appropriately.

When you see the Registry Editor, navigate to the following folder:

HKEY_LOCAL_MACHINESystemCurrentControlSetControlSession Manager
When you get there, locate the BootExecute value, as shown in Figure B, and double-click it.

Figure B

The BootExecute value launches Check Disk at startup.

As shown here, the default value data of BootExecute value should be

autocheck autochk *

If it reads anything else, simply overwrite the entry with the default value data.

To complete the operation, click OK to close the Edit Multi-String dialog box, close the Registry Editor, and restart your system. Once your system restarts, you can return to the Check Disk GUI, select both the Automatically Fix File System Errors check box and the Scan For And Attempt Recovery Of Bad Sectors check box and click Start. When the system restarts, Check Disk should run normally.

Check Disk runs at every startup

When Check Disk is scheduled to run at startup, Windows is supposed to reset the BootExecute value to its default setting as soon as the Check Disk operation is launched. If Check Disk runs at every startup, the cause is typically a configuration error or a slight corruption problem in the registry that prevents the BootExecute value from being reset to its default setting. Therefore, the first solution described above should also solve this problem.

However, if resetting the BootExecute value to its default value doesn't solve the problem and Check Disk runs again at startup, it is possible that the Dirty Bit is stuck. To check the status of the Dirty Bit, you'll use the Fsutil command.

To begin, right-click on the Command Prompt shortcut and select the Run As Administrator command. When you encounter a UAC, you will need to respond appropriately. Then type:

Fsutil dirty query Y:

Where Y: is the drive letter on your system. The result should tell you that the drive is dirty.

At this point, you'll use the Chkntfs command to disable the Check Disk operation for the next startup. Type:

Chkntfs /x Y:

Where Y: is the drive letter on your system. The result should tell you that the file system is NTFS.

To continue, close the Command Prompt and restart your system. When your system restarts, it should boot right into Windows -- you should not see Check Disk attempt to run. However, if it does, you should open a Command Prompt window and launch Check Disk in full repair mode. Type:

Chkdsk /f /r Y:

Where Y: is the drive letter on your system.

You'll then be prompted to schedule Check Disk to run at startup. To continue, type Y and press [Enter]. Then, restart Windows and allow Check Disk to run at startup. When it does, it should properly reset the Dirty Bit and Windows should start normally from this point forward.

Have you encountered Check Disk problems?

Have you encountered problems with Check Disk? If so, have you tried either of these methods? Did they work? Did you try alternative solutions? Please drop by the Discussion area and let us hear from you.

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About

Greg Shultz is a freelance Technical Writer. Previously, he has worked as Documentation Specialist in the software industry, a Technical Support Specialist in educational industry, and a Technical Journalist in the computer publishing industry.

15 comments
IcemanTheBloomy
IcemanTheBloomy

i have tried to run the program using the first method and i have failed. nothing happens. and the problem doesn't get fixed (im trying to backup my computer) plz help

Mike Williams
Mike Williams

Good info. First thing I do when I get a new PC is to a) do a full scan for bad sectors, b) restore it using the recovery media or partition as a sanity check. When I bought my wife's brand compaq laptop (about a year ago). I had a huge problem with chkdsk it would get though stages 1 to 4 ok, but stalled every time at stage 5, checking unused area for bad sectors. As this was the last one available in Best Buy I couldn't simply take it back saying it was faulty. As the point of failure was near the 128GB boundry I thought it might be a problem with Vista and the compaq's drivers so I simply re-partitioned to 120GB and 40GB and all has been fine since then. Both logical disks have chkdsked out fine since then. Regards Mike

FXEF
FXEF

If Vista can't set chkdsk to run at the proper time, why would you trust Vista and chkdsk to repair a hard drive? Just another reason Vista was released too soon... still beta quality.

megamanx
megamanx

I use a defragmenter program and it's good, but after some problems with a few programs that I installed, the program told me that there I have to do CheckDisk to clear up some issues. The CheckDisk runs fine and it fixed 2 issues. I did select both squares before going through the process. Just that when I tried the defragmenter again, it told me that I still had some issues. I was wondering if there is any way to get my problems solved anyway possible? I have Vista Home Premium, just to make that clear.

karlee_mb
karlee_mb

Very good info; quick question, however! Can I use a similar or the same process if I am encountering the same problem in Windows XP.

theHankster
theHankster

A friend's laptop experienced a "black screen" on startup that was caused by a combination of autochk.exe and NTFS's checkdisk marking a volume corrupt. (See http://support.microsoft.com/kb/952139/en-us) The machine was unbootable and I didn't have the Vista install disks. I resolved the issue by booting into UBCD4Win, opening a command prompt on the c: drive and running "chkdsk /f" from there. It prompted me to unmount the drive, which I did. After the checkdisk completed, the machine booted fine. I know that this isn't the scenario that you developed in your article, but I thought this might help someone else in my situation.

ken.klein
ken.klein

I'll look forward to trying this on my daughter's laptop the next time she brings it home from college. She was having trouble with missing files; Roxio wouldn't start, IE wouldn't start, etc. I was able to look at the directory structure but when I attempted to go into the directory to check further, the message came up that it was corrupted. I ended up taking the hard drive (SATA) out of the laptop and adding it as a second drive in a minitower. When I booted the minitower, Check Disk immediately detected problems with the "new" drive and fixed them. The laptop ran fine after that repair, but Check Disk still won't run on startup even when it is scheduled to do so.

medbiller
medbiller

Recently when I obtained my brand new Dell Latitude XT with Vista Bussiness, I upgraded windows with SP1 and installed VS2008, SQL Server 2005, VB6 and other apps. I often use. Then I decided to run Disk Cleanup just to get familiar with the OS and all my installed apps. disappeared??? Has anyone seen this?

Mark W. Kaelin
Mark W. Kaelin

Have you encountered problems with Check Disk? If so, have you tried either of these methods? Did they work? Did you try alternative solutions?

Merlin the Wiz
Merlin the Wiz

It has been my experience that the XP version of Chkdsk does not always (or even usually) correct all errors the first time it is used. I have had the same problem in XP and found that running Chkdsk on boot more than twice clears all of the reported errors.

dave01010101
dave01010101

I had a folder with a gig worth of stuff in it. I ran a checkdsk and it disappeared (but did not release any space on the drive). After a defrag or two and a full checkdsk it came back. Btw, how did you get VB6 installed? Did you have to install the VB5 runtimes first?

lorenzoxox
lorenzoxox

Sometimes when you shut your computer off by unpluging the cord from the back or by forcing your computer to shutdown, after starting it again you are going to get the chech disk screen that will check for errors in your OS. Let it finish and it wont happen again unless you force your pc to shutdown again.

pgit
pgit

Thanks. I've seen a couple vista boxes with problems I couldn't figure, and this appears to be it. The latest one was antivirus throwing errors on start. Attempting to uninstall failed with 'file not found' errors. The fellow had powered off with the 'press and hold' due to a lockup. (a game) I'm now guessing checking "lost" the files. Sounds like check disk is using some data point as it's reference of what the file system should be, and that the newly installed stuff doesn't get 'updated' into that reference. If so I would call this a registry bug. In any event, I'll give defrag and chkdisk a go next time I encounter the disappearing files routine. Thanks for the tip.

medbiller
medbiller

Actually I didn't have any problems installing any of my tools (except XSoft Spy which doesn't run in Vista).