There are a few reasons we stick to capitalization for the formal you. Teachers generally do the same when they teach Italian and Accademia della Crusca supports it. The way the program is set up would make it difficult to distinguish whether the pronoun in question is a female friend or a male you respect. Imagine having finished the first few lessons and all of a sudden you realize she means something else!
Can someone explain why you say "sta" and not "e"? When do you use "stare" and not "sei"?
please check this one, jenny: http://forum.wordreference.com/showthread.php?t=231131&langid=20
Would it not be "Come stai Lei?" if it was the formal you? Sta makes it third person
So far in this program they have not used the formal lei. Maybe they will down the road