This started just recently … i believe following last update, but not sure. System hangs for 2 mins waiting for Stop Job for User Manager 1000 … even when i log User 1000 out before reboot. I can find nothing related in Journal output.
I have researched and can find nothing that works.
Suggestions anyone?
If you’re using Plasma with Wayland, this is a known bug on Plasma 5 that is hopefully fixed in Plasma 6.
If you are really sure it is a bug and nothing important (like a service waiting to unmount a drive), there was a setting to reduce the default timeout from the default 90 or 120 seconds. 10 Seconds should do if everything works fine.
Unfortunately i do not remember in which config file it was.
I’ve had the same issue for years. KDE + X11. I had it working at some point, set it to 30 secs but then some update was released and it stopped working.
https://www.freedesktop.org/software/systemd/man/latest/systemd-system.conf.html
I have edited/added to /etc/systemd/system.conf
DefaultTimeoutStopSec=30s
DefaultDeviceTimeoutSec=30s
Both are ignored currently, it always takes 90 secs.
I don’t know if I should edit Watchdog timers as well.
I found the following in my notes. It is pretty old and I haven’t tried it to see if it works. I have seen this issue on occasion as well (xfce). So here goes. Modify as necessary. Maybe it will be of some help:
I suppose you can try a drop-in config file in /etc/systemd/.
Create a folder in etc/systemd, if one does not already exist.
/system.conf.d (/etc/systemd/system.conf.d/)
Call the file kill-fast.conf with the following contents and place in the folder that you just created:
# By default, when a service is told to stop, systemd waits 90s before SIGTERM.
#
# This might make perfect sense for servers where a database might be slow to
# shut down, and scenarios like that. However, on a simple desktop, it's
# senseless. Anything that takes over 2s to stop is just misbehaving, my
# computer needs to turn off when told to.
[Manager]
DefaultTimeoutStopSec=5s
Note that if any of your applications takes more than 3s to exit cleanly, this will result in data loss. You should have an idea of what you’re running. Push it up to 10s if you’re not sure
Thanks Teo … yes, I should have included in OP that i also tried that in /etc/systemd/system.conf … but it makes no diff.
Thanks Zhongsiu … yes changes i make to /etc/systemd/system.conf also ignored in this instance.
Thnx jrich … for the tip on possible loss of data. Indeed!
Thanks Ben … maybe Plasma6 will fix it anyway. Of interest however, when i logged out of my 1000 session to see the login screen to check for Plasma (Wyaland) option I found that there is no ‘session type’ option menu in lower LH corner … HOWEVER, when trying to log in again via the login screen the system completely freezes for 90 secs before the login is processed.
Does this give any clues?
My solution to this is totally illogical but has always worked, change the SDDM theme to either Breeze or Breathe (can’t remember which now).
Thanks CGA … so I changed SDDM theme to Breathe, rebooted and on shutdown the issue resolved … HOWEVER, since each restart of the system the pause for stop-job returns. After trying many new themes it remains hung on closing the system. 
Sorry to hear that, it’s indeed an irritating issue I struggled with for years.