If you are using SHA512 certificates with Server 2012 R2 or earlier and you use TLS 1.2 as well you will get communication errors services that are used on this certificate this includes but is not limited to
Internet Protocol security (IPsec) stand-alone
IPSec with DirectAccess
Microsoft Lync Server 2013
Remote Desktop Services (RDP)
SSL websites
SSL based VPN
Web applications
This includes the cipher suites RSA\SHA512 and ECDSA\SHA512 - to remedy this install this update:
http://support.microsoft.com/help/2975719