Blocks disappear seemingly at random.

Arbitrary formations of blocks have been disappearing from my world seemingly at random. This isn't related to the issue of entire chunks despawning; it seems to be isolated to one or two dozen blocks. The nighttime screenshot shows the damage; the daytime screenshot shows the same area from a backup world. The only change I intentionally made to the affected area was the lightning rod.

-Issue seems to happen both to blocks I've placed and naturally generated blocks

-I don't think it's Creepers; the surrounding dirt has not been damaged at all in the screenshots

-I don't think it's lightning; I'm 99% sure no thunderstorms occurred between when I placed the rod and when I noticed the damage.

-I don't think it's Endermen; I've seen blocks disappear from areas Endermen can't reach (i.e. the ceiling of a room)

-I believe (but haven't confirmed) the disappearing blocks are dropped, and can be picked up again, but they usually despawn before I notice the damage

-My world is rather large, about 1GB in file size. The affected area is close to the origin.

-My world was created before version 1.4