From the thread on airliners.net, I gather that there are two recorders. They are on a continuous two hour and two and a half hour loop respectively. In other words, we will never find out what happened in the cockpit during those critical first two hours of the flight.
There are the cockpit voice recorder (CVR), which records the last two hours' worth of audio, and the flight data recorder (FDR), which records a whole bunch of stuff about the airplane for the duration of the flight.
Unfortunately, the FDR will tell us what happened, but the CVR will likely be unable to tell us why.
The CVR will have almost two hours' worth of engine noise, followed by some minutes of relative quiet, followed by a final SPLASH! The critical, interesting words will have been overwritten and lost to history!
It seems to me likely that the plane was hijacked. Why else to turn off the transponder at such a vulnerable point? The probable intent was to fly it to some airfield in the 'stans, followed by who knows what fate for the passengers.
But then there was a fight to retake control, which somehow resulted in incapacitating all aboard who could have flown the plane or radioed for help.
What resulted was a modified Payne Stewart scenario: fly on autopilot until the fuel runs out, then go in!