In the settings menu you can configure the program's behaviour.
If the ink level of a cartridge is less or equal to the guard level, then it is marked with the blinking signal
and the program's icon in the system tray becomes
.
If this option is active, when the program starts, the main window doesn't appear, even if it may be shown by clicking the program's icon in the system tray.
When you select this option, you could also select Go to background on close. This option is useful when you want to launch the program automatically during the session start-up.
Under GNOME you could select System→Preferences→Personal→Sessions.