Frankly, I have no idea why this lag is happening, but here is how I reproduced the bug:

I'm using Intel integrated graphics 4000, and oddly, when Minecraft is windowed, everything from the menu to game play is extremely slow. When I put everything into fullscreen, though, all of the framerate lag goes away.

While windowed, I average about 1-2fps, but while in fullscreen mode, I get about 40-50fps.