There was a very good article I just read (via Facebook, can't get a link to copy, article was from wired.com).
In any case, the author speculated a fire. He went on to detail that the pilots would have shut down all electrical equipment (including transponders) in an effort to stop the fire from getting worse. He says that the apparent flight path change was to get them to an airport with an 11,000 foot runway with an approach over the ocean, as opposed to the 8,800, with a tough approach.
This is by far the best answer to this mystery. Makes the most sense. I just wonder why no one has investigated this further.