Are you using Data Store for ArcGIS or are you working with another RDBMS?
Do you see any errors in either the server or the portal logs with regard to this issue?
When you publish directly to the GIS Server, are features copied into your server managed database?
In Portal for ArcGIS, you can have any number of ArcGIS servers can be added to it.
To make one of the server as a hosting server in your portal, the hosting server should have "Server Managed Database".