That's nutty  :)

While the VM is shown as running in virt-manager, can you do:

(as non-root user)
groups
sudo virsh -c qemu:///system list --all
sudo virsh -c qemu:///session list --all

Then for any results you get,

sudo virsh -c qemu:///system dumpxml VM

(or qemu:///session if that is where they showed up) ?

Can you also post your /etc/libvirt/libvirtd.conf?

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https://bugs.launchpad.net/bugs/999681

Title:
  Afer upgrading "libvirt-bin" to  0.9.8-2ubuntu17.1 to virsh cannot
  identify  machine after reboot

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