Okay, back to the OP: I took the time and did the research, and here is the story, which comports with my memory at the time.
http://www.historycommons.org/context.jsp?item=a900hijackingaverted
I don’t know anything about that website or the provenance of the story, but this is certainly the “fifth plane” story I heard at the time, and confirms that some guys did (reportedly) vanish after behaving suspiciously (they were able to do so because the pilot took the aircraft back to the gate and told the passengers to get off as the airport was being evacuated.