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unable to run autochk on C drive on a windows server 2008 R2 Domain Controller

I have a Windows server 2008 R2 and it's a Domain Controller; It's  running as a VM on an ESXi 5.5 host. All of the volumes on this server are on the host local hard disks in RAID5.  All 5 FSMO roles are on this DC.
Okay here is the issues:
It's currently experiencing issues with installing windows updates and Symantec Backup Excec 2010 is not able to back up its System State. I see in the system event log, Event ID 55 "The file system structure on disk is corrupt and unusable. Please run the chkdsk utility on the volume C." When I rebooted the server, it would automatically Autochk or chkdsk on C:. However, it would always stuck at this message. See attached.
I wanted to know if it's safe to boot into Recovery Environment by going to "Repair My Computer" at the windows startup menu (by hitting F8 key at starup) and run chkdks /F or /R command from the command prompt. This is a DC so I wanted to be very careful. Has anyone done this before on a Windows server 2008 R2 DC in a similar situation?
Avatar of Lee W, MVP
Lee W, MVP
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You said this was a VM.  

Make a FULL BACKUP (copy the vmdk if you must) and then attach the drive to another VM and run CHKDSK from that.
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yes, it's a VM.
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Seth Simmons
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Thanks, Lee and Seth. I will put that on my list of options. Have you tried running "Repair MY computer" at F8 startup and run chkdsk /F or /R at the recovery command prompt? I wanted to do that but don't know how risky it is. It sounds like it might just be as risky as running chkdsk on it from another VM.
either that or boot from the media and choose recover and try chkdsk from there; might be less of a chance that way of C being in use.  shouldn't be any risk
In regedit navigate to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager
In the right pane find BootExecute. Double click on it.
What values does it have?