Had a similar experience at SJC 2 weeks ago - had modified the reservation online (not even time, just added XM radio) and was sent to the counter as a result. Lady at the counter said that there was absolutely no reason for me to come there and sent me directly to the cars.
Ironically, last time when my card expired and I was supposed to come to the counter to update it, I forgot to do that and went directly to Emerald Aisle. Still was processed at the exit with no problems.