The way that I see it is for the GUI to remain minimized in the System Tray upon boot.
Enabling/disabling the GUI upon boot should be a option in the EC GUI software.
If the GUI is not selected to start with windows, it should open via a Start Menu Shortcut, then close normally or you could have a option ro minimize the GUI to the System Tray, as well.
Just my two cents.
Compumind 
