GUI, entities, and world flash when in windowed fullscreen (not small window or fullscreen)

I am using Intel Graphics HD 4000 on Samsung ATIV Book 4. With Ubuntu 16.04 LTS, various objects and entities flicker in very specific circumstances. The game must be in windowed fullscreen. If it is a window (not maximized) everything is fine. If it is real fullscreen, everything is fine. Here is a video demonstrating the behavior and showing my video settings and GLX info: https://youtu.be/5aA9fHXc4rU

I have tried the Intel driver installer and adding the mesa Launchpad PPA.