Might be VLC's using a different codec, I dunno. But video processing in general is a very labor-intensive process, so even if there'd be just a small difference in processing, the overall speed could be influenced greatly.
I mean, it's 2.073.600 pixels they have to draw on screen 24 times per second, and each time it has to be calculated based on whichever codec is used - for MPEG, that involves getting the 'current' frame, apply a set of transformations to it, and display. Plus the rest. I'm nowhere near an expert on these matters, so I wouldn't even be able to begin to imagine what it takes.