Sure, I just added exec i3.

But my original one is like this:
#!/bin/sh
# /etc/X11/xinit/xinitrc
#
# global xinitrc file, used by all X sessions started by xinit (startx)
# invoke global X session script
. /etc/X11/Xsession
/usr/lib/polkit-gnome/polkit-gnome-authentication-agent-1 # &
exec dbus-launch ck-launch-session i3
[[ -f ~/.Xresources ]] && xrdb -merge ~/.Xresources
#export SUDO_ASKPASS=/bin/dpass.sh sudo -A $(dmenu_path | dmenu)
#export SUDO_ASKPASS="$HOME/bin/dpass.sh" sudo -A $(dmenu_path | dmenu)
# Start the window manager:
#if [ -z "$DESKTOP_SESSION" -a -x /usr/bin/ck-launch-session ]; then
#  exec ck-launch-session dbus-launch --exit-with-session /usr/bin/i3
#else
#  exec /usr/bin/i3
#fi
# The x11 line was already there.
# The lxpolkit line is supposed to launch lxpolkit on startup.
# The i3 line was supposed to solve the issue.
# The last one works, it's to launch the config file of urxvt.

Keep in mind that I'm sure it works both on other machines and on this same machine, but when the partition wasn't encrypted (meaning there was 3 partitions: for /, for /home and for /swap).

I don't have xorg-xinit, but I installed xorg --no-install-recommends, which also worked just fine when the partition wasn't encrypted (meaning there was 3 partitions: for /, for /home and for /swap). I do have both startx and xinit, and I don't remember on other installs if I had the .xinitrc provided as default.

I can try another WM or even a DE. But really, I see no difference with the working install and this one besides encryption, and a slightly different partitioning scheme.

Up to this point, we eliminated:
* config files (ownership and permissions, disabling some of them like bashrc and xinitrc) * completely removing i3 an launching startx gives me a tty with a different font, and the keyboard behaves just the same (inactive, numpad led always on or off, depending on how it was befre launching startx)
* reinstalling xorg. Maybe purge xorg wasn't enough?
* encryption shouldn't be an issue since the partition is opened before reaching the tty. * Maybe I've made a mistake during the install, but besides having a separated /boot, I did nothing out of the ordinary. Plus I have no boot issues anyway. /root (including another /boot partition without the initialization option), /home and /swap are just logical volumes of the same encrypted volume group.

What I can also try is to redo a non-encrypted install, but with the exact same partitioning scheme and see how it goes.

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