I personally think this has to do with VBO, i Have the problem aswell, GTX 770 Here, latest NVidia drivers etc.
Confirm this, this does also happen to me on interacting with doors or other blocks. The door graphically stays shut, but i can walk through it. Sometimes, it fixes itself after a while.
This also occurs on some actions in the overworld. Opening a door, or breaking a random block etc.
@Blah I vanaf confirm that, I have VBO off, and the problem isn't solved. The same thing happens