Under Building Blocks, Equipment & Codes how many Project Components do you have? The Extender IR Port is assigned at the Project Component level. If you have no Project Components or everything is in a single Project Component (because you had all your IR codes in 1 activity during import), this is your problem. I can easily change the IR port on same extender by clicking on different Project Components.

F1 Help also has information about working with Components spread across the Quick-Start Wizard and Building Block Topics.