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Chkdsk through vista locks up but from cd runs and completes.

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I was working on a customers computer today and they were running a chkdsk /r in Vista which got stuck at 60 percent and would go no farther. This was weird to me because usually a chkdsk will run and come back as either failed or completed not stuck. I was able to start into normal mode and ran a few scans including Malware Bytes and SAS which deleted a few things but only adware no trojans or anything to serious.

I then tried chkdsk /r again and it ran and got stuck at the same spot. I then put in a Windows Vista Basic DVD and ran chkdsk /r from the dvd. It completed successfully without any errors on the volume. I then started back up into Windows thinking Widows must be the problem but to be sure I ran Western Digital Diagnostics. It is a Western Digital HardDrive. The diagnostics passed and everything seemed normal. I then ran SFC /scannow which did say Vista had errors but was unable to fix them all. I have never seen one in Vista come back saying it didn't have errors.

I believe that the chkdsk file is messed up somehow and I was wondering if there is anyway to fix it without reinstalling Windows. We had 3 seperate opinions on the matter and nobody could think of anything. Anyone know of something to try for future reference?

The computer was a Gateway Laptop with Windows Vista Basic. The hard drive was a 250GB Western Digital. I don't know the computers specs more than that sorry guys.
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    Kraków my love :)

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I then ran SFC /scannow which did say Vista had errors but was unable to fix them all

Vista creates sfc log.
Navigate to C:\Windows\Logs\CBS folder. You'll see CBS.log file.
See, what errors couldn't be fixed.
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