Its the city that Jet Blue picked. They actually have a good number of connecting passengers to and from SJU at JFK. T6 is a bit tight and they approached T4 for some temporary relief. They were able to work out a way for the SJU arrival to depart right back to SJU which gets rid of the need to tow plans to and from T6 for the flights. And yes, every once and a while an international arrival will take out an early morning SJU departure.

SJU passengers tend to have larger bags than say an MCO pax and this was one other consideration....remove a flight that puts extra preseure on your baggage system.