Well, have you actually checked your video player? Many players and web browsers exactly behave like you describe to compensate for Retina displays so stuff doesn't appear super tiny...
So Quicktime might actually be zooming the display when it should be viewing at actual size?
Still having trouble here? Let us know.
Thanks for following this up. I came to the conclusion that playing the video through the Quicktime player on my iMac was displaying a 200% view instead of actual size, due to the retina display. I hope I'm right in thinking this.
Viewed at 100% in After Effects it looked to be exactly the right size (based on the pixel count of my screen), but viewed at "actual size" in my Quicktime player after rendering it was 2 x the size.