So this issue happens to all 23.976Hz files (from PAL XVID to 4k h.265).
Sometimes it helps to just jump to the Desktop, but it helps everytime to open the Windows resolution menu.
See here a video of the situation (sometimes I had problems playing the video in VLC and it looks more choppy than it is in real, but it should be good enough to show what happens):
https://dl.dropboxusercontent.com/u/58997187/2017.02.19-14.43.mp4
Also attached the logs I generate while the recording.