Just ran through the Enterprise Builder process to set up an Enterprise Base Deployment of 10.6.1 on Windows Server 2012 R2. It's nice that the Builder packages up the install and makes it very convenient, but the documentation (also possibly the Server Install Guide) should include a post configuration reminder that you should consider also installing an Enterprise Database Client to the host server. I just ran through a support case to have a Support Tech tell me that I hadn't installed a SQL Server Client on the server because my symptom was that I couldn't register an enterprise geodatabase in the ArcGIS Server data store. There is reference to this in the part of the Server Documentation that talks about registering databases, but it's not in the installation guide portion of the documentation. In step 8 of the Server Installation Guide, it talks about making your data accessible to ArcGIS Server, but it doesn't explicitly say you've got to have an Enterprise Database Client on the server to make that happen.
So, how about including reminders in the installation guides for Builder and Server that once you're done configuring the server applications, you should really consider adding the appropriate Enterprise Database Client to the host server as a final step, because publishing map services on a fresh install aren't going to go well if the ArcGIS Server can't see the Enterprise Geodatabases (yeah that was as rhetorical statement). enterprise builderarcgis server and arcgis enterprisearcgis enterprise installation