Comment 24 for bug 1531224

That tread was very helpful.
But you mixed things up.
I also experience the same problem with flickering background in greeter.

But, my story starts differently.
When I first time installed Xubuntu 16.04 and set up desktop background, greeter was showing it without any problem.

Then, I created xorg.conf.d, and specify "Monitor" "Device" "Screen", and after this my greeter background starts to blink.
But it is not just blink.
SNA somehow remembers desktop background and draws it again, but LightDM greeter redraws it and this process looks like flicker.
If you specify in greeter: user-background=false, with SNA you will see background and then greeter will clear it.

So the solution is to add option: user-background="do nothing"

Also I found out that with SNA I can't wakeup my monitor, because xrandr loses "current" mode
To wake it up I need to connect via ssh and manually set monitor mode:
xrandr -d :0 --output HDMI2 --mode 0x47

After this mouse movements wake up my monitor.

SNA is crappy.