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Chkdsk running frequently on 2012 r2 server and trashing it

Hi

As above.  We have two similarly spec'd VMs running 2012 and running a number of applications.  Currently after installing windows updates and restarting were finding that the server is chkdsk'ing and breaking a number of apps.  A restore is fixing this and then a retry of updates works fine.
Were backing up these two VMs with different backup products, veeam and acronis, so assume its not to do with this...
Ideas what can be checked to see what the issue is here before we build new VMs and migrate apps?

Thanks
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J S
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Are you sure it's CHKDSK that's running and causing the servers to crash?  If you are sure then you can simply verify that by killing the  CHKDSK process when it happens.

Do you have any VM snapshots running?
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No USB and no snapshots.
Cant seem to find the download link for the ultimatebootcd..
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did you read what i posted?
go to the download page, scroll down to the mirror section, and  click on a mirror to start the download
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@ nobus: yes i found the link and downloaded it, however it doesn't appear to run any checks that i can see in the menu..
@jason: yes these are VMs
post a screenshot - or picture of the menu you see