FAA (well JFK TWR anyway) seem to think it was a fire:
IDENTIFICATION
Regis#: BAW116 Make/Model: B747 Description: B-747-400
Date: 12/30/2005 Time: 0453
Event Type: Incident Highest Injury: None Mid Air: N Missing: N Damage: Unknown
LOCATION
City: NEW YORK State: NY Country: US
DESCRIPTION
ACFT RETURNED TO LAND ON RWY 31L AFTER TOWER OBSERVED FLAMES ON LEFT SIDE OF ACFT, NEW YORK, NY