This seems to happen on Win 10 Creators Update with some NVIDIA cards when vsync is disabled in the game settings (and d3d9 is on).
One of the solutions: enable vsync in the game settings, but force-disable it in the NVIDIA control panel for WA. This may not feel the same as with the previous setup.
Another possible (untested!) solution: Right-click WA.exe, select Properties - Compatibility - "Disable full-screen optimizations". This is new and untested, and because I can not reproduce this issue on my system, I ask everyone who is/was affected by the issue to try this out (disable any of your current workarounds first). This may have something to do with the new Game Mode on Windows 10.
Edit: this doesn't work according to Asbest, FaD and Tiku.