Alaska has a link to more info on Secure Flight on the main page of their website. They also mention SF in the hold message when you call their reservations line. I believe that the hold message mentions a specific date when the program starts (I think it said August 1st).

If they aren't set up to deal with it yet, then why don't they clearly communicate that message? Telling people what they need to do to comply, then not giving them the ability to comply by not printing the middle initial on the BP is really confusing.