I can confirm this. For my Lenovo ThinkPad T450s with 2 external
monitors, it is exactly the same. Drove me nuts for the better part of a
day until I realized it was due to 4.9.0-4. As such I'm also back to
running 4.9.0-3 as a workaround.
In my case I would only* get the flickering (ie. the screen/monitor
goes blank for a sec or two) in the following scenario:
1) move mouse cursor inside of my GNOME Terminal window
2) use the keyboard to type something (anything)
*With the mouse cursor hovering outside of my term window, I was safe
so to say. Having said this, occasionally a monitor would also flicker
when moving the mouse cursor from one external monitor to another.
B/R,
Frederik Dannemare