The Global Inbox is a Favorite folder, so you are asking to display a specific Favorite folder when eM Client starts, but not to display Favourites. You need to choose a startup folder other than the Global Inbox (All Inboxes).
There is a consistency bug in the UI that does not allow you to turn off the favorites folder in the SETTINGS menu, but does allow you to turn off favorites if you unselect by right clicking the inbox.
You have to have “Show Favorites” selected to use “all inboxes” in this menu, and you can’t turn it off unless you deselect “All inboxes”
Yes that message is actually correct. You cannot normally de-select / uncheck Favorites in Settings with All Inboxes still selected in the Startup, as All Inboxes normally needs Favorites enabled to work.
So to disable Favorites select “Inbox as your Startup” as per the below. Then save settings.