My services show as 'stopping' in the arcgis server 10.3.1 manager after the upgrade from 10.2. In the admin page the status reads as started for the configuration state and stopped for the real time state. I can't publish a new service as there is error that my publishing service isn't started and i can't start it using any of the available ways. Is there anyone with the same issue?
If anyone else has the same issue you can fix it by making sure that the ArcGIS server site is referencing the local name of your machine not the dns alias. The server was getting confused between the two names thinking they were two different machines.
I had the same problem. Stopping and starting ArcGIS Server service from Task Manager solved the problem.