USA Today has a much more detailed story.

Interesting facts in this story:

The "HJK" was in message traffic sent to company by the plane, David Greenberg says it was routine traffic about where to divert to in light of the closing of US airspace following the morning hijackings. ARINC was going through old traffic from that morning and found it.

Somehow, controllers and the flight crew miscommunicated - the story said controllers tried asking the plane "coded questions" to determine whether they were hijacked, and the plane ended up squawking 7500. The story speculates that the crew may have misunderstood the questions as an order to set the transponder.

Sounds like a royal screwup, and the story, if accurate, reflects badly on everybody, though it's understandable given the panic at the time.