Nick, I was initially puzzled by your comment that some Audyssey measurements used the same position as another measurement. This wouldn't appear to be helpful, since each measurement has to be of at least a slightly different room environment. Dr. Kyriakakis has emphasized that the measurements shouldn't be widely separated in an attempt to "average" over a large listening area. He mentions positions clustered around the main listening spot, separated maybe a foot or two apart.
The study you link largely follows this pattern, but makes the basic setup with even less separation(e.g., 3-6"). Note though that all the positions are in fact different, being either to the side, the front or above(purple)the other positions.
