I started an update, authenticated, then minimized the window. When I returned to it nothing seems to have happened. So I tried it again and this time kept the window open. It was displaying a backend error for a couple of seconds and then hide them again.

Depending on the fatality of an error it probably should not autohide them as the user might not be reading them in time. 
Additionally it most certainly should not autohide while the window isn't even visible.