I don't have an explanation of the behavior of pam-auth-update, but
Debian bug #923362 has also just been filed regarding pam_systemd
inexplicably getting disabled, and may be related.

** Bug watch added: Debian Bug tracker #923362
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=923362

** Also affects: pam (Debian) via
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=923362
   Importance: Unknown
       Status: Unknown

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https://bugs.launchpad.net/bugs/1817897

Title:
  attempting to enable fingerprint with pam-auth-update breaks gdm

Status in pam package in Ubuntu:
  New
Status in pam package in Debian:
  Unknown

Bug description:
  I ran sudo pam-auth-update, enabled "Fingerprint authentication",
  selected "OK", and then rebooted.

  GDM wouldn't start after the reboot:

  Feb 27 06:29:41 jik-x1 /usr/lib/gdm3/gdm-wayland-session[1551]: 
dbus-daemon[1553]: [session uid=121 pid=1553] Activating service 
name='org.freedesktop.systemd1' requested by ':1.0' (uid=121 pid=1551 
comm="/usr/lib/gdm3/gdm-wayland-session gnome-session --" label="unconfined")
  Feb 27 06:29:41 jik-x1 /usr/lib/gdm3/gdm-wayland-session[1551]: 
dbus-daemon[1553]: [session uid=121 pid=1553] Activated service 
'org.freedesktop.systemd1' failed: Process org.freedesktop.systemd1 exited with 
status 1
  Feb 27 06:29:41 jik-x1 /usr/lib/gdm3/gdm-wayland-session[1551]: Unable to 
register display with display manager

  I logged in on a VT and ran pam-auth-update again. I observed that
  "Register user sessions in the systemd control group" was not
  selected, even though my recollection was that it had been selected
  before I enabled fingerprint authentication, and I didn't disable it.

  I unselected fingerprint authentication and selected "Register user
  sessions in the systemd control group" and rebooted again. GDM started
  working again.

  ProblemType: Bug
  DistroRelease: Ubuntu 19.04
  Package: libpam-runtime 1.3.1-5ubuntu1
  ProcVersionSignature: Ubuntu 4.19.0-13.14-generic 4.19.20
  Uname: Linux 4.19.0-13-generic x86_64
  ApportVersion: 2.20.10-0ubuntu21
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Wed Feb 27 06:31:32 2019
  InstallationDate: Installed on 2019-02-26 (0 days ago)
  InstallationMedia: Ubuntu 18.04.2 LTS "Bionic Beaver" - Release amd64 
(20190210)
  PackageArchitecture: all
  SourcePackage: pam
  UpgradeStatus: Upgraded to disco on 2019-02-26 (0 days ago)

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