The article mentions runway 4L was being used for takeoffs. In the ATC communications, you can hear them say "American 185, runway 31L at KE, line up and wait" before telling Delta 1943 to cancel their takeoff clearance. And after the near collision, ATC tells American 106 Heavy "we're departing runway 4L."

Wouldn't the line up and wait call for American 185 mean that they were departing from both 4L and 31L?