I received an alternate today as well, for the Directing program.
I just shot them back a quick e-mail, expressing my great interest, though I know for a fact that the people in the office actually don't choose the alternates, the professors do (they told me as much in the interview).
Man, this makes for a sticky situation, doesn't it? Haha
Though, from what they told me in the interview, they accept exactly as many fellows as the program allows (28 for directing, I think) and then the rest go into alternate, they apparently don't "over-accept", in that they don't officially accept more people than they have slots for in the program. I remember them telling me "if you get accepted, please realize that we, the teaching faculty, spent a lot of time deciding on your application, and that we carefully choose each of the people who get into the opening positions", so they seem to take the whole process very seriously.
And from what I can tell from older posts, people from the AFI alt list get in fairly often, so there is definitely some hope for us, eh?