New users not showing up while trying to set folder permission settings

Server 2012
This is a new virtual domain server and file server in a starwind cluster, I just started migrating users last week.
 This last weekend (two days ago) the cluster crashed while doing windows updates on this server. I have been unable to get it to download any updates since without crashing, not sure if that is related to this issue somehow.
I added some new users today and got them all logged in and their data transferred over. good. But then I went to this shared folder that everyone has a mapped drive too and tried to add them in the security tab of a sub folder but their accounts will not show
up when I search for them. Any account I added previously to last weekend  show up, students, mine, etc.
even if I select the exact OU the accounts are located in, even if I type their whole name and domain. In AD the accounts are there.
If I log into the backup domain controller Their accounts show up there while in a folder security settings tab. They are listed in active directory on both domain controllers.
I have exhausted myself on Google search.
What the heck did I break?
Maybe I should run 
DISM.exe /Online /Cleanup-image /Restorehealth
Not sure if I will lose any data doing that or what the repercussions would be..

Hi Dustin,
If the DC is having USN rollback issue, we can resolve it by demote then re-promote or restore the DC using a supported method such as using System State backup to restore.
More information for you:
USN Rollback, Virtualized DCs and improvements on Windows Server 2012
http://blogs.technet.com/b/reference_point/archive/2012/12/10/usn-rollback-virtualized-dcs-and-improvements-on-windows-server-2012.aspx
Best Regards,
Amy
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