I've been having the same issue with the special Windows 10 version of OneNote. OneNote 2016 works without issues.
Supposedly, if you have this issue in 2016, you can disable hardware graphics acceleration in the advanced options, but that setting doesn't exist on the UWP version.
For me, simply closing and reopening OneNote wasn't enough to fix it (it also happened in any other Modern app). Rebooting the computer worked, but that's a hassle. I did find a quicker workaround, though.
Open up Task Manager and kill Desktop Window Manager. Windows will complain and all that, but once it's killed (it restarts itself automatically), my screen stops flashing.
I really hope Microsoft fixes this...