I put this itinerary in the AS website as a multi-city flight (which allows up to four segments) and applied the companion fare discount code and it seemed to work just fine. I used random dates next July; the primary ticket was about $1120 and the companion ticket was about $220 with taxes.
I have a companion cert as well and ran this itinerary too. Assuming WAS means DCA, random dates in July, open jaw between JNU and SIT, stopover in SEA, and it works. Traveller 1 came in at $1229 (probably the dates I chose) and the companion is $103.76. Taxes are $118.40. Total for 2 passengers is $1451.16. Not bad. If you can swing it, you can bump up to first class on the DCA-ANC and SEA-DCA legs for a total of $2108.08.
Have fun!