Hi and welcome to Sysnative. Let's see if this gets you fixed up.
Step#1 - SFCFix Script Warning: this fix is specific to the user in this thread. No one else should follow these instructions as it may cause more harm than good. If you are after assistance, please start a thread of your own.
Download SFCFix.exe (by niemiro) and save this to your Desktop. If you still have this on your desktop from downloading previously, you don't need to re-download.
Download the file below, SFCFix.zip, and save this to your Desktop. Ensure that this file is named SFCFix.zip - do not rename it.
Save any open documents and close all open windows.
On your Desktop, you should see two files: SFCFix.exe and SFCFix.zip.
Drag the file SFCFix.zip onto the file SFCFix.exe and release it.
SFCFix will now process the script.
Upon completion, a file should be created on your Desktop: SFCFix.txt.
Copy (Ctrl+C) and Paste (Ctrl+V) the contents of this file into your next post for me to analyse please
SFCFix version 3.0.0.0 by niemiro.
Start time: 2016-12-29 08:40:49.807
Microsoft Windows Server 2008 R2 Service Pack 1 - amd64
Using .zip script file at C:\Users\sierra\Desktop\SFCFix.zip [0]
PowerCopy::
Successfully took permissions for file or folder C:\Windows\Winsxs\amd64_microsoft-windows-mprapi_31bf3856ad364e35_6.1.7601.17514_none_72328a5b69a4257a\mprapi.dll
Successfully took permissions for file or folder C:\Windows\Winsxs\amd64_microsoft-windows-mmsys_31bf3856ad364e35_6.1.7601.17514_none_bc95cfaff5caa70e\mmsys.cpl
Successfully took permissions for file or folder C:\Windows\Winsxs\amd64_microsoft-windows-mmres_31bf3856ad364e35_6.1.7600.16385_none_bacb7329f882f019\mmres.dll
The file \\?\C:\Windows\Winsxs\amd64_microsoft-windows-mprapi_31bf3856ad364e35_6.1.7601.17514_none_72328a5b69a4257a\mprapi.dll is in use and must be replaced over a reboot.
Successfully copied file C:\Users\sierra\AppData\Local\niemiro\Archive\Winsxs\amd64_microsoft-windows-mmsys_31bf3856ad364e35_6.1.7601.17514_none_bc95cfaff5caa70e\mmsys.cpl to C:\Windows\Winsxs\amd64_microsoft-windows-mmsys_31bf3856ad364e35_6.1.7601.17514_none_bc95cfaff5caa70e\mmsys.cpl.
Successfully copied file C:\Users\sierra\AppData\Local\niemiro\Archive\Winsxs\amd64_microsoft-windows-mmres_31bf3856ad364e35_6.1.7600.16385_none_bacb7329f882f019\mmres.dll to C:\Windows\Winsxs\amd64_microsoft-windows-mmres_31bf3856ad364e35_6.1.7600.16385_none_bacb7329f882f019\mmres.dll.
Successfully pended file for replace over reboot: \\?\C:\Windows\Winsxs\amd64_microsoft-windows-mprapi_31bf3856ad364e35_6.1.7601.17514_none_72328a5b69a4257a\mprapi.dll
Successfully restored ownership for C:\Windows\Winsxs\amd64_microsoft-windows-mmsys_31bf3856ad364e35_6.1.7601.17514_none_bc95cfaff5caa70e\mmsys.cpl
Successfully restored permissions on C:\Windows\Winsxs\amd64_microsoft-windows-mmsys_31bf3856ad364e35_6.1.7601.17514_none_bc95cfaff5caa70e\mmsys.cpl
Successfully restored ownership for C:\Windows\Winsxs\amd64_microsoft-windows-mmres_31bf3856ad364e35_6.1.7600.16385_none_bacb7329f882f019\mmres.dll
Successfully restored permissions on C:\Windows\Winsxs\amd64_microsoft-windows-mmres_31bf3856ad364e35_6.1.7600.16385_none_bacb7329f882f019\mmres.dll
PowerCopy:: directive completed successfully.
Reboot:: directive completed successfully.
PostRebootCorruptionDetection::
No hash verification failures detected.
PostRebootCorruptionDetection:: directive completed successfully.
PostRebootRestorePermissions::
Successfully restored ownership for C:\Windows\Winsxs\amd64_microsoft-windows-mprapi_31bf3856ad364e35_6.1.7601.17514_none_72328a5b69a4257a\mprapi.dll
Successfully restored permissions on C:\Windows\Winsxs\amd64_microsoft-windows-mprapi_31bf3856ad364e35_6.1.7601.17514_none_72328a5b69a4257a\mprapi.dll
PostRebootRestorePermissions:: directive completed successfully.
Successfully processed all directives.
SFCFix version 3.0.0.0 by niemiro has completed.
Currently storing 3 datablocks.
Finish time: 2016-12-29 08:46:11.640
----------------------EOF-----------------------
This will create a file, cbs.txt on your Desktop. Please attach this to your next post.
Please Note:: if the file is too big to upload to your next post please upload via a service such as Dropbox or One Drive or SendSpace and just provide the link.
I investigated further during the holidays. The raid 1 had a bad disk. I have replaced it, successfully rebuilt the raid and now the server will pass SFC.