This appears to completely resolve the problem for me!
Screen flicker on 16.04. Screen goes black for an instant intermittently. Not happening previously on 15.10. System was upgraded from 15.10, not a fresh install from ISO.
tlp settings appear to affect the problem. This worked for me:
In file /etc/default/tlp, change the following settings to match.
USB_AUTOSUSPEND=0
USB_AUTOSUSPEND_DISABLE_ON_SHUTDOWN=1
Run $ sudo tlp start
That should fix it.
Lots of trial and error, but this has fixed the problem completely for me. If someone can tell me how the USB controller is causing the screen to flicker black intermittently, I’d love to understand it better. 
If screen flicker comes back after suspend/resume cycle, try:
$ sudo tlp init restart
and if that doesn’t work, try:
$ sudo tlp init force-reload
There are two systemd services around tlp: tlp.service and tlp-sleep.service. It appears that tlp-sleep.service is responsible for managing events around suspend/resume, so maybe something with that isn’t working quite right. I think we can tweak the sleep service and make this fix more robust. If someone else doesn’t do it first, I’ll post a fix back here when I find one.
If you were bitten by this issue, you probably have this one too: "Crackling" sound whenever sound starts to play