You will need to first set up Script Manager in the Admin session, which is the session that is being accessed while running as a service.
When you open Script Manager as an application, make sure you right click on the shortcut and Run As Administrator. Once you do that you will notice that the databases are not yet set up or configured. Manually configure them again but leave them open, then click Server - Exit. Then start the Script Manager service again. You can verify that it is running by checking the logs. There should be a line that states Monitoring Operations Started.
If you still have trouble or the service still doesn't seem to be working, please open a new Support Request.
Software Support Manager
Support Team Fortis – Americas