Treadmills, grindstones and noses
I'm not qualified to comment on pair programming, but here's a theory about how agile methods increase productivity for rather mundane reasons.
Despite all the waffle about ownership and empowerment, one of the ways in which methods like Scrum improve productivity is simply be exposing every developer's efforts to the team. In a waterfall environment you get a piece of work and a relatively long slice of time to do it. Depending on your outlook, you may get it all done quickly then spend the rest of the time surfing, or spend most of the time surfing then get it all done even more quickly. In agile development, the smaller tasks and reporting to the daily stand-up tend to cut down on the time spent goofing off*.
I wonder if pairing enhances this effect? The two developers are unlikely to conspire to spend part of their time doing nothing much, so their noses stay in contact with the grindstone and the treadmill keeps on turning.
* I wish to make it clear that I personally think the goofing off time is when your brain does its best problem-resolving work. YMMV.