Johna, by check-in, does that mean you gave your boarding pass to the gate agent?

I would only think you would you would have a concern if you gave your boarding pass to the agent and it was such a full flight that they had to do a head count.

I would then think that the airline would subject you to the terms of your FF agreement. Here is what Delta says:
http://www.delta-air.com/skymile/guide/index.html