Embedded in the updates that rolled out during August's Patch Tuesday (or, Update Tuesday, as Microsoft now refers to it), there's a change in how Windows Server 2012 R2 Essentials handles Office 365 or Windows Azure Active Directory services.
Prior to the update, environments with more than a single domain controller could not integrate Azure Active Directory or Office 365 for the organization. There's been no real explanation on why it was this way, just that it was.
For those with multiple domain controllers installed in the organization that want to take advantage of either Azure AD or Office 365 integration, you'll want to take a closer look at the August 2014 update rollup (KB2975719) for Windows RT 8.1, Windows 8.1, and Windows Server 2012. The fix is bundled in the rollup.