The data they looked at showed a large drop in the worldwide crow population. So no, it definitely wasn't just at that prison.

My thought is something along these lines. We see the crows in Somalia drop out of the sky in 1991, and they're in the vicinity of this huge tower. Presumably the tower is also responsible for the loss of consciousness reported in that region. I would guess that the crows only die en masse within a certain range of the "signal broadcast" or what-have-you... which would imply that there were lots of places broadcasting for the worldwide blackout. This would also explain why a lot of crows died, but not all crows. And since this is the first time anyone's mentioned dead crows, they haven't been looking yet to see if this was reported in other areas.

Now, why didn't that boy black out when the crows died in 1991? It looked like the tower was in the middle of (or right outside) a town or village of some sort. Possibly that town is the only place where the blackout occurred in 1991 - the boy might have been out of the then-limited range.