Remember that Alaska never guarantees a seat assignment. They are all only seat requests. For that reason, don't expect the ticket counter agent to have a ton of pity on you either. I'm sure they'd love to help, however there is little they can do. You may have lost your seat for many reasons... computer error, equipment change, etc. It is always best to check your reservation a couple days after booking to see if your seat request actually went through. If not, get the next best seat.

Its probably too late, but for future reference, to keep you from wasting time in line waiting to speak with an agent, check in on the ITM machine and when it shows your seat assignment press the button that says "change seat." The map it shows you is the same that the agent will look at (except it doesn't offer emergency exits.) You may find something better than your original seat! If not, take the next best seat and ask the agent at the gate if they can do anything. They have more control over seat assignments than counter agents. Cheers!