I have the very same issue with my 2016 MacBook Pro 13" (Touchbar). This only happens when a Parallels VM (Win 10) is running. Disabling DirectX is not really a solution as the performance is so bad that I can't really work. I hope you guys get this sorted out quickly, otherwise I have to go back to VMware Fusion...
One more detail: it seems that the flickering mostly starts right before the machine is going into sleep mode (when the display dims).
Last edited: Jan 13, 2017