On a fresh installation of Debian Stretch with GNOME 3.22 configured in debian-installer with a French locale and a French keyboard layout, when I login for the first time with my new user (hence there's no ~/.config/dconf/ yet) gnome-shell is started with the "us" keyboard layout active (instead of the expected "fr" one).

But the keyboard layout menu shows "French" first and "English (US)" second (as does gnome-control-center) and the correct value is stored in dconf in org.gnome.desktop.input-sources.sources. localed is also reporting "fr" as the recommended keyboard layout.

$ dconf dump /org/gnome/desktop/input-sources/
[/]
sources=[('xkb', 'fr+latin9'), ('xkb', 'us')]
xkb-options=@as []
$ localectl status
   System Locale: LANG=fr_FR.UTF-8
       VC Keymap: n/a
      X11 Layout: fr
       X11 Model: pc105
     X11 Variant: latin9

A simple gnome-shell restart (with ALT+F2 r) is enough to get the French keyboard layout active by default. In Debian, we are not using gnome-initial-setup so the gsettings for input-sources is set by gnome-settings-daemon on first login.

I'm not sure how this can be explained... maybe a concurrency issue between gnome-shell and gnome-settings-daemon where gnome-shell picks the "us" layout by default because gnome-settings-daemon has not yet set the correct value? And then when the good value is set, it stays on the current keyboard layout instead of switching to the default one?

I filed this on gnome-shell because it seems the most likely culprit here but it might be that this needs to be fixed somewhere else. Feel free to move around as appropriate.

NB: This also affects very badly Debian live images: the user configuration does not persist across reboots and gnome-shell is thus always started with the undesired keyboard layout.