You may get the subject prompt only when you have set any of the profiles in Second Copy to "also run at shutdown".
Instead of shutting down the computer from the Start menu, please try the "Exit and Shutdown" option from the Second Copy icon in the system tray next to the clock by right mouse clicking on it.
When you right mouse click on the Second Copy icon in the system tray and select shutdown/restart/logoff, it handles the 20-second Windows limitation for the shutdown. When you use the Start button to make your shutdown selection, Windows does not report this selection to Second Copy and therefore Second Copy prompts you to re-select it so that it would remember to execute your selection after running the profiles that are set to run at shutdown.
