From your description, it seems you closed the GSX menu from Toolbar, instead of using the Hotkey or the X icon on it. That results in GSX not being able to pop-up menus to wait for something, resulting in procedures skipped, like in that case.
As the manual explains, when the use of the menu is discussed at Page 74:
This is now your normal workflow should be:
• Open the GSX menu from the Toolbar icon when first starting Ground services.
• Don’t close it from the Toolbar while Ground services are performed, always use the Hot-key or the X icon to close the menu.
• Close the menu using the Toolbar icon when you are done with Ground services, usually before take-off.
In brief, the Toolbar Icon should always be left Active while Ground services are required.