Some airlines like mine (I allows non revenues to arrive at check-in without listing, but it helps very much to the agent to check you in if you are already listed, because they can automaticaly display your name and destinations, and print your boarding passes.
Some airlines like Continental didnt want me to check me in once because i wasnt listed on a flights, so they kindly sent me to the ticketing counter for listing and them comming back.
It is just a matter of rules. And I think they are very easy to follow... Arent they?