This is known issue, but to remember myself for next versions: If you run EMS for Exchange 2013 SP1. Error comes out:
It has 3 possible issues. Here are solutions:
Root cause 1:
Exchange server is out of sync with time of DC. You should always have the following hierarchy of time sync in your domain: Reliable time source -> PDC -> Other DCs -> Servers and clients
- Disable windows time sync from physical host if it is virtual machine
- Enable time sync with domain by the following commands:
- On PDC
net stop w32time
w32tm /config /syncfromflags:manual /manualpeerlist:0.pool.ntp.org
w32tm /config /reliable:yes
net start w32time
On other DCs and Servers:
net stop w32time
w32tm /config /syncfromflags:domhier /reliable:no /update
net start w32time
Root cause 2:
Exchange server path to kerbauth.dll is wrong / Powershell virtual directory is misconfigured. I have re-created virtual directory for Powershell on affected server:
Get-PowerShellVirtualDirectory -Server <AffectedServer> | Remove-PowerShellVirtualDirectory
New-PowerShellVirtualDirectory -Server <AffectedServer> -Name PowerShell
Get-PowerShellVirtualDirectory -Server <AffectedServer> | Set-PowerShellVirtualDirectory -BasicAuthentication:$false
IISReset
After virtual directory re-creation I have checked its modules in IIS and made sure, that Kerberos module is native and the path to its DLL is correct:

Root cause 3:
There is a missing Windows feature WinRM IIS extension.The full description is here: http://technet.microsoft.com/en-us/library/dd759166.aspx This was the case in my lab and I feel it is the side effect of in-place upgrade of OS from Windows server 2012 to Windows Server 2012 R2 on Exchange server (Yes I know it is not good idea, but how to learn non standard issues in other way). Here is simple solution: Install this windows feature:
Get-WindowsFeature *IIS* #to check if it is installed
Add-WindowsFeature Winrm-IIS-Ext # to install
