I love the fact that APOD posted this photo today. It's a great mystery. One of the explanations I've heard is that the dark streak is the shadow of a contrail and the apparent flash over the water is unrelated to it. I believe (but can't remember for sure) that the photographer was just snapping happily and didn't see anything happen until the print was examined and this "event" was captured.
BTW, take a look at a previous APOD when one of my photo composites was featured! (shameless plug)
I've read through some of the discussions, and the shutter speed was 1/19 (?), and the other photos were taken in fiarly quick succession, maybe seconds or minutes.
One explanation I saw that I could buy into - a bug flew in front of the lens, and the bright spot is where it was when the flash went off.
I have examined all three frames and I determine they are no more than 1 min from first to third shot. You can tell by the towering thundercloud as it builds. You can obtain the large picture of the streak photo by going to //antwrp.gsfc.nasa.gov/apod/image/0412/strange_pryde_big.jpg. Put each one in your browser and click first, second, third. You can see the cloud formation change [slightly] and the boats remain in the same position [maybe not moving, but I believe they are] showing a very small amount of time had passed between shots.
Now take in to consideration that anything that size hitting the water would make a wake that would go outward in a oblong direction towards the travel of the object. If you look at frame three there is no wake or wave.
Conclusion: This is not a solid object hitting the water or leaving the water [as in missile]. However I can’t explain it but my best guess would be something flying in front of the camera as a bug that was captured.
Look closely at the post and tree. The flash effect slightly stars out around the post and the tree/bush seems unaffected at all by the change in light at that location. The central flash has a 1 o'clock to 7 o'clock flare that is exactly 90 degrees to the streak.
Almost appears more that a model rocket in that general area was launched upward (without an arch mind you) from the surface of the water. But the lack of flare on the bush seems to me to say this flash event did not happen quite so near to the lens.