Volcano

Sorry for the serial posts, but a lighter Dragon would also theoretically transmit a greater portion of the aerodynamic forces through to the second stage. And non-Dragon launches have a fairing that might reduce the forces on the interior of the second stage. So this mission really could have involved the greatest compressive stress applied to the second stage so far, which maybe it just can't handle. Obviously I'm speculating here, but that's all any of us can do until we have answers...

Thinking about it further, maybe the "counterintuitive cause" was too SMALL a payload? I haven't looked at all F9 missions, but it seems that CRS-7 included the smallest payload among F9 v1.1 CRS missions. Smaller payloads would mean higher acceleration, i.e., higher G-forces. And the failure occurred between Max-Q (highest aerodynamic forces from the nose) and MECO (highest acceleration, I think). Thus, the squeeze on the second stage between the first-stage engines and the nose cone might have been higher than in any prior launch. Thoughts?

The F9's exhaust plume is so gigantic that journalists are using pre-RUD photos to depict the explosion: http://www.wsj.com/articles/SB12367224787933994021304581062191281870326 (though the white spot on the second stage might be the beginning of it)

That makes too much sense, for it to be a "counterintuitive cause."