try doing multi trips ANC-JNU and JNU-SEA. It usually shows up some milk runs that way
I tried doing ANC-JNU and JNU-SEA on multi trips....it shows flight 62 for ANC-JNU but won't show flight 62 as an option for JNU-SEA. I've noticed if the flight # is the same, alaskaair.com generally won't let you book them as two separate segments.