When you manually start the agents the NeoLoad Web configurations are stored under that folder: C:\Users\<USERNAME>\AppData\Roaming\Neotys\NeoLoad\v6.9\conf
Inside the properties files you will find all your settings including the zone information.
When you start the agents as Windows Service there's no icon in the System systray. Nevertheless the same configuration files are stored in the System user profile. The path of that folder dépends on the OS version but it should be something like this: C:\Windows\System32\config\systemprofile\AppData\Roaming\Neotys\NeoLoad\v6.9\conf
So you'll find in that folder the exact same properties files <agent|controller_agent>_user.properties. You just have to copy the ones mentionned above instead of these ones and restart your Services.
Let me know if it's not clear enough.