UA 1542 21-Jan, EWR-BOS, 737-900 (20 J seats). Showed "Checked-in full" prior to flight. I was in paid F, one of two GS that boarded during pre-board. About ten minutes before the door closed, a gentleman came up and sat in the empty seat behind me, showing the FA his BP had changed. But two other seats, 4A and 4B, remained empty at door-closing, with about 20 on the upgrade list. The GA did not come in to upgrade anyone, nor did the FA do anything. So we flew all the way from EWR-BOS (44 minutes!) with two open F seats.