faster than the speed of sound in air, whereas the 3rd wouldn't even be a true shockwave, it would be a subsonic gust of wind which would have shaken the plane much later on. In this case, the first 2 shockwaves would be supersonic i.e. My guess is that there could have been another 'shock' much later than the first 2, which would be just the gust of air/wind caused by the huge temperature and pressure change in the blast pushing air outward in all directions. I'm not sure about the accounts of a 3rd shockwave. These are the 2 first shockwaves that tail gunner Bob Caron directly saw with his eyes approaching the plane from behind The first 2 shockwaves are easily understood enough: the first is the shockwave directly from the explosion over Hiroshima and the second is the reflected shockwave that bounced off the ground and hit the plane shortly after. 2 shockwaves vs 3 shockwaves), but since you haven't got an answer yet, I'll throw in my best guesses (would be interested in more input here though).
I've searched around and found conflicting accounts of the number of shockwaves felt by the Enola Gay (i.e. This past July, the last surviving crew member of the Enola Gay, the plane that dropped Little Boy, died in Stone Mountain, Georgia, having given many interviews.