I've opened MC 1.9 in fullscreen mode, cause it was set to on, and pressed F11 when the game was fully loaded, so it changed back to the small rectangle. But then I couldn't change the screen size anymore. I'm only able to change the screensize to the little rectangle that will be made automatically or to Fullscreen. This error only occures if you start MC with the settings "Fullscreen: ON" enabled.
Feel free to comment and question if I was not clear.