Even when you are protected, you still need to check-in for that flight at least 30 minutes before departure. The agents have no idea where you are if you aren't checked-in, so they will dump your seat and give it to someone else who they know is there. Since you can only be checked into one flight at a time, sometimes you actually need to choose which flight you want if the flights are scheduled to leave very close together. In the OPs case, his seat was given away because he didn't check-in in time to claim the seat the 1K desk had reserved him.