The plane sits at GRU all day for an evening return, so it's the flight that can be delayed with no further operational consequences. If mechanical failures leave them a plane short (or crew re-scheduling due to other delays leaves them a crew short) at JFK, they'll delay this flight rather than any other.

This explanation would also apply to the other GRU flights, so a disparity is an indication that there is less availability of spares (relative to the need for them) at JFK.