Multiple Displays in 10.12

I have a quad core i7 Mac Mini running 1 Thunderbolt Display and 1 HDMI display. Have been running this for a year or more with no issues. Update to 10.12 and instantly start having issues where the Thunderbolt Display will flash, meaning it goes black then the image will come back. Disconnect the HDMI display and things work fine. Reached out to Apple Support via Twitter and they had me check firmware and stuff, no resolution. They switch me to a "Specialist". Still no resolution. I have an older i5 Mac Mini still running 10.11. Both monitors work fine. Update to 10.12 on the i5 Mac Mini and have exact same issue. Thunderbolt Display flashes. Again reach out to Apple "Specialist"... The specialist actually asked me how i was connecting the Thunderbolt Display to my Mac Mini... I said are you serious... The Thunderbolt Display will only connect via a Thunderbolt connection as there are no other ways to connect... Back to the story... I feel this is related to 10.12 since it replicated on 2 different machines but worked fine prior to installing 10.12. Apple insist it is not software related but some hardware issue. They want me to schedule an appointment at the Genius Bar which the closest Apple Store is 4 hours away... Has anyone else had any issues running dual monitors in 10.12?

Thanks,
Bobby