flightaware.com/live/flight/AAL1639 
From KJFK To TJSJ Its normal flight time is 3 Hr. 50 min. and this flight is going to take 5 Hrs 51 minutes in a Boeing 757-200 !
Is this the flight you are talking about? flightaware.com/live/flight/AAL1 … /KJFK/TJSJ
from aa.com
AMERICAN AIRLINES - Flight #1639 FLIGHT STATUS - ARRIVED
Detailed Flight InformationAMERICAN AIRLINES Departing
JFK New York 07/10/2009 7:30 PM 11:44 PM
Arriving
SJU San Juan 07/11/2009 11:45 PM 3:15 AM
Looks like multiple original flight plans confusing FA. The flight was 4 hours late (I think) but the times still don’t add up. Isn’t PR one hour ahead of NY ?