qrexec-daemon will start new processes for called services, which
include starting new DispVM, starting other required VMs (like backend
GPG VM). Having those processes as root leads to many permissions
problems, like the one linked below. So when VM is started by root, make
sure that qrexec-daemon will be running as normal user (the first user
in group 'qubes' - there should be only one).
QubesOS/qubes-issues#1768