A lot of people have been having issues with this as seen in a qubes forum post and a qubes reddit post (I can’t include links)
I am also having this issue. It started a few days ago after using the qubes update tool.
all VMs or only specific one (e.g. sys-net, sys-firewall)?
All whonix-ws-16 based appVMs besides disposables
how long did those VM run before you try to shutdown?
Any length of time, it does not matter. The issue always occurs.
how do you shut them down?
Use the upper right blue Q button, hover over the vm, and then click shutdown
what template are they based on?
whonix-ws-16 (but disposables are able to shut down)
how do you know they restart / are running?
I get a notification that the vm is shutting down, and then right away I get a notification that the vm is starting up.
are you using any testing repositories?
Security testing only.
which Qubes OS release are you using (R4.0 or R4.1)?
I saw some people have suggested that a vm could be requiring these whonix-ws-16 based vms, which is why they restart after shutdown. But that can’t be the case, because then they would be started right away. And I can run just sys-whonix, sys-firewall, and sys-net. Nothing auto starts. But when I open a whonix-ws-16 vm, I can not shut it down after. So I think that proves no other vm is using it?