This problem has occurred on 16.10 which is why I decided to stick with 16.04. Now with the 16.04.2 update, I'm getting the same issue.
Once in a while, very randomly (most noticeable while in the Terminal using the up key to get to a previous command or using the backspace key) my whole screen flickers black.
Before with Ubuntu 16.04.1, I didn't have that problem. I would update to Kernel 4.6 and install the Intel Graphics Update Tool and everything worked perfectly. Doing the same (without the Kernel update) on 16.04.2 does the same thing as other distros with Kernel 4.8 (or Ubuntu Gnome at 4.6).
Given I don't get the issue on the LiveDVD I tried not installing any drivers but that didn't help.
I've also tried adding i915.enable_psr=0 and i915.enable_rc6=0 to GRUB to no avail.
Can anyone help me please?