(not to mentioned is run with user 136 which is likely lightdm)

Recently, I noticed errors on some LXC containers regarding missing /run/user/XX directory, without paying much attention.

But on a desktop machine, /run/user/1000 was missing recently and it led me to find out that even though elogind is installed and registered console login, it does not register X session with lightdm.

loginctl
SESSION UID USER SEAT TTY   STATE  IDLE SINCE
     22   0 root -    pts/0 active no   -   

1 sessions listed.
# ps aux | grep lightdm
root      1092  0.0  0.0   6548  2400 pts/0    S+   14:57   0:00 grep lightdm
root     22437  0.0  0.0 380968  7128 ?        SLl  14:11   0:00 /usr/sbin/lightdm
root     22445  2.5  0.6 25633760 214312 tty7  Ssl+ 14:11   1:08 /usr/lib/xorg/Xorg :0 -seat seat0 -auth /var/run/lightdm/root/:0 -nolisten tcp vt7 -novtswitch
lightdm  22482  0.0  0.0   4468  2180 ?        S    14:11   0:00 dbus-launch --autolaunch 88d78492ae7aa04b49d29220687f7529 --binary-syntax --close-stderr
lightdm  22483  0.0  0.0   5684  1692 ?        Ss   14:11   0:00 /usr/bin/dbus-daemon --syslog-only --fork --print-pid 5 --print-address 7 --session
root     22494  0.0  0.0 169752  7980 ?        Sl   14:11   0:00 lightdm --session-child 13 24

On another similar desktiop system, I get:

# loginctl
SESSION  UID USER    SEAT  TTY   STATE   IDLE SINCE
      1 1005 wark    seat0 tty7  active  no   -   
     16    0 root    -     pts/0 active  no   -   
     c1  136 lightdm seat0 -     closing no   -   

3 sessions listed.

# ps aux | grep lightdm
root      3924  0.0  0.0 307288  7172 ?        SLl  12:20   0:00 /usr/sbin/lightdm
root      3932  2.8  0.2 25496504 89184 tty7   Ssl+ 12:20   4:23 /usr/lib/xorg/Xorg :0 -seat seat0 -auth /var/run/lightdm/root/:0 -nolisten tcp vt7 -novtswitch
lightdm   4173  0.0  0.0   4512  2124 ?        S    12:20   0:00 dbus-launch --autolaunch 4edebaaa884f554dc8f3e050493a2ab4 --binary-syntax --close-stderr
lightdm   4174  0.0  0.0   5736  1852 ?        Ss   12:20   0:00 /usr/bin/dbus-daemon --syslog-only --fork --print-pid 5 --print-address 7 --session
lightdm   4176  0.0  0.0 380748  6896 ?        Sl   12:20   0:00 /usr/libexec/at-spi-bus-launcher
lightdm   4182  0.0  0.0   5700  3244 ?        S    12:20   0:00 /usr/bin/dbus-daemon --config-file=/usr/share/defaults/at-spi2/accessibility.conf --nofork --print-address 11 --address=unix:path=/run/user/136/at-spi/bus_0
lightdm   4198  0.0  0.0 167628  7276 ?        Sl   12:20   0:00 /usr/libexec/at-spi2-registryd --use-gnome-session
root      4354  0.0  0.0 170228  8164 ?        Sl   12:20   0:00 lightdm --session-child 13 24
root      5966  0.0  0.0   9748  2276 pts/0    S+   14:57   0:00 grep lightdm

No so lightdm seat0 and no user seat0 on the first one. And I compared installed software and both PAM and lightdm config without noticing any differences.

I found no recent bug report and IA neither provided insights.

Any clue what is going on?