They may have held them on board because of not having immigration available. Seems there was another case similar to what you describing. Regardless I believe that it still violates the three hour tarmac rule.
Edit:
http://www.cnn.com/2010/TRAVEL/12/28/jfk.stuck.tarmac/
http://news.travel.aol.com/2010/06/2...ane-for-hours/