Here is an excerpt of the journal during a 90 second shutdown (actually a reboot but the result is the same). Look at the timestamps to see where it occurs. The complete log is posted here for your convenience.
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Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) UnloadModule: "libinput"
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) systemd-logind: releasing fd for 13:69
Aug 05 22:37:59 C2 systemd[1]: Stopped CUPS Scheduler.
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) UnloadModule: "libinput"
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) systemd-logind: releasing fd for 13:68
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) UnloadModule: "libinput"
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) systemd-logind: releasing fd for 13:67
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) UnloadModule: "libinput"
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) systemd-logind: releasing fd for 13:65
Aug 05 22:37:59 C2 dbus[568]: [system] Activating via systemd: service name='org.freedesktop.Accounts' unit='accounts-daemon.service'
Aug 05 22:37:59 C2 dbus[568]: [system] Activation via systemd failed for unit 'accounts-daemon.service': Refusing activation, D-Bus is shutting down.
Aug 05 22:37:59 C2 gdm3[752]: Failed to contact accountsservice: Error calling StartServiceByName for org.freedesktop.Accounts: GDBus.Error:org.freedesktop.systemd1.ShuttingDown: Refusing activation, D-Bus is shutting down.
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) UnloadModule: "libinput"
Aug 05 22:37:59 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) systemd-logind: releasing fd for 13:66
Aug 05 22:37:59 C2 gdm3[752]: GLib: g_hash_table_find: assertion 'version == hash_table->version' failed
Aug 05 22:37:59 C2 systemd[1]: Stopped GNOME Display Manager.
Aug 05 22:37:59 C2 systemd[1]: Starting Show Plymouth Reboot Screen...
Aug 05 22:37:59 C2 systemd[1]: Stopped /etc/rc.local Compatibility.
Aug 05 22:37:59 C2 systemd[1]: Stopped target Network is Online.
Aug 05 22:37:59 C2 systemd[1]: Stopped Network Manager Wait Online.
Aug 05 22:38:00 C2 systemd[1]: Received SIGRTMIN+20 from PID 2490 (plymouthd).
Aug 05 22:38:00 C2 systemd[1]: Started Show Plymouth Reboot Screen.
Aug 05 22:38:00 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) NVIDIA(GPU-0): Deleting GPU-0
Aug 05 22:38:00 C2 /usr/lib/gdm3/gdm-x-session[1180]: (WW) xf86CloseConsole: KDSETMODE failed: Input/output error
Aug 05 22:38:00 C2 /usr/lib/gdm3/gdm-x-session[1180]: (WW) xf86CloseConsole: VT_GETMODE failed: Input/output error
Aug 05 22:38:00 C2 /usr/lib/gdm3/gdm-x-session[1180]: (WW) xf86CloseConsole: VT_ACTIVATE failed: Input/output error
Aug 05 22:38:00 C2 /usr/lib/gdm3/gdm-x-session[1180]: (II) Server terminated successfully (0). Closing log file.
Aug 05 22:38:00 C2 systemd[1]: Stopped Session 3 of user system.
Aug 05 22:38:00 C2 systemd[1]: Removed slice User Slice of system.
Aug 05 22:38:00 C2 systemd-logind[576]: Removed session 3.
Aug 05 22:38:00 C2 systemd[1]: Unmounted /run/user/1000.
Aug 05 22:39:29 C2 systemd[1074]: at-spi-dbus-bus.service: State 'stop-sigterm' timed out. Killing.
Aug 05 22:39:29 C2 systemd[1]: session-c2.scope: Stopping timed out. Killing.
Aug 05 22:39:29 C2 systemd[1]: session-c2.scope: Killing process 1081 (Xorg) with signal SIGKILL.
Aug 05 22:39:29 C2 systemd[1074]: at-spi-dbus-bus.service: Killing process 1098 (at-spi-bus-laun) with signal SIGKILL.
Aug 05 22:39:30 C2 systemd[1074]: at-spi-dbus-bus.service: Main process exited, code=killed, status=9/KILL
Aug 05 22:39:30 C2 systemd[1074]: Stopped Accessibility services bus.
Aug 05 22:39:30 C2 systemd[1074]: at-spi-dbus-bus.service: Unit entered failed state.
Aug 05 22:39:30 C2 systemd[1074]: at-spi-dbus-bus.service: Failed with result 'timeout'.
Aug 05 22:39:30 C2 systemd[1074]: Stopped target Basic System.
Aug 05 22:39:30 C2 systemd[1074]: Stopped target Paths.
Aug 05 22:39:30 C2 systemd[1074]: Stopped target Timers.
Aug 05 22:39:30 C2 systemd[1074]: Stopped target Sockets.
Aug 05 22:39:30 C2 systemd[1074]: Closed GnuPG network certificate management daemon.
Aug 05 22:39:30 C2 systemd[1074]: Closed GnuPG cryptographic agent and passphrase cache (restricted).
Aug 05 22:39:30 C2 systemd[1074]: Closed GnuPG cryptographic agent (access for web browsers).
Aug 05 22:39:30 C2 systemd[1074]: Closed Sound System.
Aug 05 22:39:30 C2 systemd[1074]: Closed GnuPG cryptographic agent (ssh-agent emulation).
Aug 05 22:39:30 C2 systemd[1074]: Closed D-Bus User Message Bus Socket.
Aug 05 22:39:30 C2 systemd[1074]: Closed GnuPG cryptographic agent and passphrase cache.
Aug 05 22:39:30 C2 systemd[1074]: Reached target Shutdown.
Aug 05 22:39:30 C2 systemd[1074]: Starting Exit the Session...
Aug 05 22:39:30 C2 systemd[1074]: Received SIGRTMIN+24 from PID 2510 (kill).
Aug 05 22:39:30 C2 systemd[1075]: pam_unix(systemd-user:session): session closed for user Debian-gdm
Aug 05 22:39:30 C2 systemd[1]: Stopped User Manager for UID 120.
Aug 05 22:39:30 C2 kernel: nvidia-modeset: Freed GPU:0 (GPU-f46a9fa1-e13e-5c6a-4b2e-746f0126ccba) @ PCI:0000:01:00.0
Aug 05 22:39:30 C2 systemd[1]: Stopped Session c2 of user Debian-gdm.
Aug 05 22:39:30 C2 systemd[1]: session-c2.scope: Unit entered failed state.
Aug 05 22:39:30 C2 systemd[1]: Removed slice User Slice of Debian-gdm.
Aug 05 22:39:30 C2 systemd[1]: Stopping Login Service...
Aug 05 22:39:30 C2 systemd[1]: Stopping Permit User Sessions...
Aug 05 22:39:30 C2 systemd[1]: Stopped Permit User Sessions.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Remote File Systems.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Remote File Systems (Pre).
Aug 05 22:39:30 C2 systemd[1]: Stopped target NFS client services.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Network.
Aug 05 22:39:30 C2 NetworkManager[590]: <info> [1501987170.1835] caught SIGTERM, shutting down normally.
Aug 05 22:39:30 C2 systemd[1]: Stopping Network Manager...
Aug 05 22:39:30 C2 systemd[1]: Stopping WPA supplicant...
Aug 05 22:39:30 C2 systemd[1]: Stopping Raise network interfaces...
Aug 05 22:39:30 C2 systemd[1]: Stopped WPA supplicant.
Aug 05 22:39:30 C2 NetworkManager[590]: <info> [1501987170.2060] exiting (success)
Aug 05 22:39:30 C2 systemd[1]: Stopped Raise network interfaces.
Aug 05 22:39:30 C2 systemd[1]: Stopped Network Manager.
Aug 05 22:39:30 C2 systemd[1]: Stopping D-Bus System Message Bus...
Aug 05 22:39:30 C2 systemd[1]: Stopped D-Bus System Message Bus.
Aug 05 22:39:30 C2 systemd[1]: Failed to propagate agent release message: Transport endpoint is not connected
Aug 05 22:39:30 C2 systemd[1]: Failed to propagate agent release message: Transport endpoint is not connected
Aug 05 22:39:30 C2 systemd[1]: Stopped Login Service.
Aug 05 22:39:30 C2 systemd[1]: Stopped target User and Group Name Lookups.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Basic System.
Aug 05 22:39:30 C2 systemd[1]: Stopped Forward Password Requests to Plymouth Directory Watch.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Slices.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Paths.
Aug 05 22:39:30 C2 systemd[1]: Stopped CUPS Scheduler.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Sockets.
Aug 05 22:39:30 C2 systemd[1]: Closed CUPS Scheduler.
Aug 05 22:39:30 C2 systemd[1]: Closed UUID daemon activation socket.
Aug 05 22:39:30 C2 systemd[1]: Closed Syslog Socket.
Aug 05 22:39:30 C2 systemd[1]: Closed Avahi mDNS/DNS-SD Stack Activation Socket.
Aug 05 22:39:30 C2 systemd[1]: Closed PC/SC Smart Card Daemon Activation Socket.
Aug 05 22:39:30 C2 systemd[1]: Closed D-Bus System Message Bus Socket.
Aug 05 22:39:30 C2 systemd[1]: Stopped target System Initialization.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Swap.
Aug 05 22:39:30 C2 systemd[1]: Stopped Apply Kernel Variables.
Aug 05 22:39:30 C2 systemd[1]: Stopped Load Kernel Modules.
Aug 05 22:39:30 C2 systemd[1]: Stopping Load/Save Random Seed...
Aug 05 22:39:30 C2 systemd[1]: Stopping Update UTMP about System Boot/Shutdown...
Aug 05 22:39:30 C2 systemd[1]: Stopped target Encrypted Volumes.
Aug 05 22:39:30 C2 systemd[1]: Stopped Forward Password Requests to Wall Directory Watch.
Aug 05 22:39:30 C2 systemd[1]: Stopping Network Time Synchronization...
Aug 05 22:39:30 C2 systemd[1]: Removed slice User and Session Slice.
Aug 05 22:39:30 C2 systemd[1]: Stopped Load/Save Random Seed.
Aug 05 22:39:30 C2 systemd[1]: Stopped Update UTMP about System Boot/Shutdown.
Aug 05 22:39:30 C2 systemd[1]: Stopped Network Time Synchronization.
Aug 05 22:39:30 C2 systemd[1]: Stopped Create Volatile Files and Directories.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Local File Systems.
Aug 05 22:39:30 C2 systemd[1]: Unmounting /home...
Aug 05 22:39:30 C2 systemd[1]: Unmounting /run/user/120...
Aug 05 22:39:30 C2 systemd[1]: Unmounting /mnt/ramdisk...
Aug 05 22:39:30 C2 systemd[1]: Unmounting /tmp...
Aug 05 22:39:30 C2 systemd[1]: Unmounted /run/user/120.
Aug 05 22:39:30 C2 systemd[1]: Unmounted /tmp.
Aug 05 22:39:30 C2 systemd[1]: Unmounted /mnt/ramdisk.
Aug 05 22:39:30 C2 systemd[1]: Unmounted /home.
Aug 05 22:39:30 C2 systemd[1]: Reached target Unmount All Filesystems.
Aug 05 22:39:30 C2 systemd[1]: Stopped File System Check on /dev/disk/by-uuid/9536bca4-419a-4862-a590-f319ecf70fb3.
Aug 05 22:39:30 C2 systemd[1]: Removed slice system-systemd\x2dfsck.slice.
Aug 05 22:39:30 C2 systemd[1]: Stopped target Local File Systems (Pre).
Aug 05 22:39:30 C2 systemd[1]: Stopped Create Static Device Nodes in /dev.
Aug 05 22:39:30 C2 systemd[1]: Stopped Remount Root and Kernel File Systems.
Aug 05 22:39:30 C2 systemd[1]: Reached target Shutdown.
Aug 05 22:39:30 C2 systemd[1]: Reached target Final Step.
Aug 05 22:39:30 C2 systemd[1]: Starting Reboot...
Aug 05 22:39:30 C2 systemd[1]: Shutting down.
Aug 05 22:39:30 C2 systemd[1]: Hardware watchdog 'iTCO_wdt', version 0
Aug 05 22:39:30 C2 systemd[1]: Set hardware watchdog to 10min.
Aug 05 22:39:30 C2 kernel: watchdog: watchdog0: watchdog did not stop!
Aug 05 22:39:30 C2 kernel: systemd-shutdow: 36 output lines suppressed due to ratelimiting
Aug 05 22:39:30 C2 systemd-shutdown[1]: Sending SIGTERM to remaining processes...
Aug 05 22:39:30 C2 systemd-journald[243]: Journal stopped
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loginctl session-status c2
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c2 - Debian-gdm (120)
Since: Sat 2017-08-05 22:32:39 EDT; 5min ago
Leader: 1061
Seat: seat0; vc1
TTY: /dev/tty1
Service: gdm-launch-environment; type x11; class greeter
State: closing
Unit: session-c2.scope
`-1081 /usr/lib/xorg/Xorg vt1 -displayfd 3 -auth /run/user/120/gdm/Xauthority -background none -noreset -keeptty -verbose 3
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (**) Option "fd" "43"
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (**) Option "fd" "44"
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (**) Option "fd" "43"
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (II) systemd-logind: got pause for 13:65
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (II) systemd-logind: got pause for 13:67
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (II) systemd-logind: got pause for 13:66
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (II) systemd-logind: got pause for 13:68
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (II) systemd-logind: got pause for 13:64
Aug 05 22:32:50 C2 /usr/lib/gdm3/gdm-x-session[1079]: (II) systemd-logind: got pause for 13:69
Aug 05 22:37:59 C2 systemd[1]: Stopping Session c2 of user Debian-gdm.
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systemctl list-jobs
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JOB UNIT TYPE STATE
1477 systemd-user-sessions.service stop waiting
1557 remote-fs.target stop waiting
1537 systemd-tmpfiles-setup-dev.service stop waiting
1515 cups.path stop waiting
1548 nfs-client.target stop waiting
1509 cryptsetup.target stop waiting
1576 remote-fs-pre.target stop waiting
1589 final.target start waiting
1496 wpa_supplicant.service stop waiting
1577 systemd-modules-load.service stop waiting
1463 user@120.service stop running
1533 systemd-remount-fs.service stop waiting
1473 local-fs-pre.target stop waiting
1512 systemd-sysctl.service stop waiting
1456 systemd-reboot.service start waiting
1579 umount.target start waiting
1490 sockets.target stop waiting
1483 systemd-update-utmp.service stop waiting
1521 cups.socket stop waiting
1480 systemd-logind.service stop waiting
1517 pcscd.socket stop waiting
1458 user.slice stop waiting
1503 system-systemd\x2dfsck.slice stop waiting
1562 paths.target stop waiting
1582 mnt-ramdisk.mount stop waiting
1470 systemd-tmpfiles-setup.service stop waiting
1464 session-c2.scope stop running
1491 dbus.socket stop waiting
1462 user-120.slice stop waiting
1455 reboot.target start waiting
1478 nss-user-lookup.target stop waiting
1500 NetworkManager.service stop waiting
1563 systemd-random-seed.service stop waiting
1581 run-user-120.mount stop waiting
1504 systemd-fsck@dev-dis…\x2d4862\x2da590\x2df319ecf70fb3.service stop waiting
1507 local-fs.target stop waiting
1568 sysinit.target stop waiting
1551 avahi-daemon.socket stop waiting
1584 tmp.mount stop waiting
1482 systemd-ask-password-plymouth.path stop waiting
1505 home.mount stop waiting
1508 systemd-ask-password-wall.path stop waiting
1495 dbus.service stop waiting
1574 uuidd.socket stop waiting
1534 swap.target stop waiting
1527 syslog.socket stop waiting
1526 systemd-timesyncd.service stop waiting
1522 basic.target stop waiting
1457 shutdown.target start waiting
1535 networking.service stop waiting
1541 slices.target stop waiting
1561 network.target stop waiting
52 jobs listed.
Here's a bug report of the same issue from Red Hat users also using Gnome (except that they get the "stop job" message and I don't). It remains unfixed.
It's worth mentioning that this issue DOES NOT occur if I first logout my account and then shutdown the computer from the login screen. I've tried some of the fixes mentioned on the internet (e.g. disabling coredump, using X instead of Wayland for GDM) without success. Any suggestions about what I should do next?