While bisecting an unrelated kernel bug I found that some kernels between 4.9.0 and 4.10-rc1 allowed: service lxdm stop to work as expected and cleanly stop the X server. Otherwise either a kill -9 of the lxdm and Xorg process or a reboot is needed to start the X server again. If it would be helpful I could try bisecting to find the commit that stopped X shutting down cleanly.