Because Script Runner on Windows runs as a service, it will have trouble accessing all the user specific settings you can define in an Adobe® application like, (print) presets, actions, etc.
To work around this, you can stop the Script Runner service, prevent it from starting up automatically and run the Script Runner as an application for the logged in user. This should also be the user you defined your presets with.
Open the Script Runner Preferences application (go to Start > All Programs > Esko > Automation Engine Script Runner > Preferences).
Stop the Script Runner and uncheck Start at login checkbox (which actually means Start as service).
Close the Preferences application.
Start up the Script Runner as a console application by simply double clicking its executable: <Script Runner’s program folder>\bin_ix86\egscrrun.exe (e.g.: C:\Esko\bg_prog_fastserverscrrunnt_v120\bin_ix86\egscrrun.exe). Now you’re good to go.
To prevent having to start up the Script Runner every time you log in, you can add its executable to your user’s/system’s StartupItems. (copy this egscrrun.exe shortcut to the autostart folder).