It looks to be related to this report:
https://bugzilla.redhat.com/show_bug.cgi?id=1088619
Workaround idea was from comment 37.
The hanging process in Qubes VM is most likely dconf-service, but there
is a lot of possible causes. To start with a non-standard method of
accessing the X session (no real login manager, processes started by
qrexec-agent). So instead of wasting a lot of time on digging through
gnome services, simply shorten the stop timeout - the processes would be
killed anyway.
1e842c985d