Now launch the app, sign in, uncheck the preference, wait a second (so the helper agent shuts down), then check it again. When the dialog opens to choose the scripts folder, don’t change the directory, just select the Choose button at the bottom of the dialog. It should now be set to the correct directory.
At that point close the Preferences window at test your key combination for Secret Agent. If it’s still not working, go back into Preferences and update the key combination preference to ensure the right keys.