We have a new corporate Portal (10.3) which is on IIS/Win2008, SSL-only with Windows-Authentication, federated and hosted (with Oracle). Most all the parts are now working, but creating a layer from a CSV file (with X,Y points) is giving strange errors. There is no map-service shown on the Portal contents, but you can see it via the REST end-points. The feature-service shows up on the portal, but is not fully usable. The various log files show errors like 'ERROR: code:403, User does not Permission to access "*.mapserver". Utilities/PrintingTools.GPServer Access is forbidden, regardless of authorization. You can see a similar 403 in the IIS logs, but why? Everything else seems to work.
We (ESRI and I) are working a hypothesis that the strange behaviors come from network latency. We have some log recordings to support this. The next step will be to try the datastore product, basically putting the 'host' DB on the actual portal server machine. This should eliminate latency as an issue.