Ensure you NOT just get a boarding pass but at Seoul station right next to the Asiana and Korean Air counters is an immigration mini office, you need to go in there and have them process your passport for exiting Korea. That process allows you to use the City Check in line for security.

Again as earlier mentioned only Korean/Asiana/Jeju support check in at City and Seoul station. Seoul station check in: its down two levels from the main station area (to the left of the escalators BEFORE the ticket gates)