Crudely put, triple buffering.
Borderless Windowed mode is not full screen as far as Windows is concerned. In Windows, if you run your application in full screen mode, the application controls how its rendered to the display device.
From Windows Vista onwards, the OS has a desktop composition feature. If your application runs in a windowed mode, the output is first rendered to a separate memory surface, then rendered into a desktop image. This is controlled by the Desktop Window Manager.
This behaviour means that the game gets the use of an extra buffer to render to, compared to the two buffer system most commonly used by game developers. A third buffer can even out the delivery of frames to the display, in some cases this helps remove hitching or stuttering in the rendering out of frames. The computer basically gets "more time" to create its frames before they have to be shown on screen.
The downside to this is that latency between what's happening in the game and what's shown on screen will increase. This may or may not be noticeable by the player. This is my guess as to what's happening anyway. I don't have the tools to prove it.