I think Exiled is onto something. This was a coordinated attack, and I suspect partially thwarted in the US, but some how, some way, the Boston bomber slipped through.

It makes sense that vague warnings from the Saudi intelligence agencies or the Pakistani ISI were just enough to get the feds around the decoy bomb at the JFK library, then some more vague warning about the marathon finish line, so rather than panic the finish line area with a massive shutdown, they moved in force to investigate and contain if possible, but shutting down every single major event that is the subject of a bomb threat means shutting down the country, to the extent that anyone making a prank call can cause the same effect as a terrorist with a real bomb.

I would also guess that if there were simultaneous attacks in several cities in the sandbox, that someone outside the US is screaming with glee from the rooftops about their successes of yesterday, but that's what will forever be blacked out of the mainstream media.