I got the solution.
The curios thing is that I wrote it myself in this post two month before:
I was not aware that there was a connection between a non working scanner and screen flickering.
Ubuntu MATE comes with tlp by default. In Xubuntu and other Ubuntu flavors it is not installed by default.
But from the beginning:
Tested with Xubuntu 16.04, Ubuntu Gnome 16.04 and Lubuntu 16.04
I undock the notebook and connect the external display. Nothing flickers. I put the notebook in the ultrabase dock, connected the dock with the external Monitor and nothing flickers at all. I plug in the usb keyboard to the dock and it starts flickering. This was the moment I thought about the USB_AUTOSUSPEND option in /etc/default/tlp, but tlp wasn't installed.
So I installed tlp and set USB_AUTOSUSPEND to 0 and the flickering at the external monitor is gone.
No video driver, not a display manager and no kernel was the problem. It was the power management.
On Ubuntu MATE I set USB_AUTOSUSPEND to 0 after installation to get my scanner working, so I never noticed it.