libvirt.img was created at boot, which means it didn't exist before, not the that explains it but any reason you're not using the cache for that?
Try moving the system folder to cache (set to cache="prefer", disabled services and run the mover), then set libvirt path to /mnt/cache/system/libvirt.img instead of mnt/user/system.libvirt.img, then reboot and post new diags if it happens again.