This is just a wild-eyed guess, but if there were a spider web or wasp's nest inside the burner, and conditions were just right, it could lead to gas/air not going where it should, not lighting properly, forming a cloud of gas outside the water heater burner, and exploding when the cloud DID hit the igniter. As i said, conditions would have to be just right, and it's a long shot, but I think I'd have a look-see at the burner for clogs or foreign material, and watch it closely while it goes through an ignition cycle to see that it works right.