Its how the agency submits your frequent flyer information. Sabre (Alaska's system) requires it to come across and link it to AS/AA. I find it faster/easier to remove it from your Alaska reservation and add it manually via the website; that ensures everything is correct. This is because Alaska's system isnt' a ONE and done deal - there's multiple systems looking at your number.

Example: the entry I use when flying AA is FFAA1234567 (and that's how its stored in the system)

But when you are flying on Alaska, it is FFAA1234567/AS when flying AS - that will make it come over correctly. *updated to show I'm using an AAdvantage number.