FLIGHT 93 CONSPIRACY THEORIES -- which involve the idea that the plane was shot down, but that it's being covered up -- make a lot of the timing discrepancy between the seismic record of the crash and when the voice recorder data end. But the seismic data are also inconsistent with the shoot-down theory according to this item in Discover magazine:
Based on the amount of seismic energy, Wallace could estimate how the plane came down: "The UA flight produced a significant signal, consistent with a fully-loaded jet that was intact, or nearly intact, on impact." That finding disputes rumors that the hijacked jet was shot down, he says, because a missile or other explosion would have broken the craft into smaller pieces that would have caused less seismic disturbance. The Pan Am crash over Lockerbie, Scotland, which blew apart in midair, produced only a faint signal, even though the crash occurred close to an array of ground-motion sensors. David McCormack, a seismologist at Natural Resources Canada who studied the Lockerbie crash, agrees with Wallace's interpretation. "To detect a signal even marginally, the aircraft would have to be intact," he says.
I've found the shoot-down / coverup theory rather flimsy anyway. I don't see how to put the pieces together in a way that makes sense. Why would the government lie about shooting down the plane? They were getting flak, readers may recall, for not shooting down the others.