I've gotten similar issues talking to customer service agents about a Starlux ticket I purchased on Alaska. The agents would refer to the JX table and say since the fare code isn't listed on the JX table, it doesn't earn miles. Even though I purchased it on the AS website, and there's no way to choose a specific fare bucket, and it certainly does not make clear it would be ineligible for miles (while also advertising 100% miles minimum).
I'm stil waiting in my case but regardless I think Alaska should be making it a lot more clear through the booking process if they're going to play this game.