I am not convinced that the "FST" we're seeing in season 6 is actually running parallel to the original timeline as most people seem to think it is. Sorry if my explanation is a bit confusing but i'll try and keep it simple(ish).
OK, so we have 2 sets of events going on at the moment. In plot A, Oceanic 815 crashes and all the stuff on the island, getting off the island and going back etc all happens. In plot B Oceanic 815 lands in LA and the story unfolds as we're seeing in the season 6 off the island scenes. If we use flight 815 as a starting point for the 2 different plots to begin, we have only a week or so onward so far to see what's going on in plot B but several years worth in plot A. My point is, if these two sets of events are running alongside each other, how can the characters in plot B be recalling things that won't be happening in Plot A until a much later date? For example, Locke doesn't write the note to Jack saying "i wish you'd believed me" until 2007 (plot A) yet in 2004 (plot B) he's aware of it.
I don't actually have a full explanation for what's going on but it seems that maybe the FST actually happens after the original timeline and the characters are remembering stuff that happened to them in the past instead of looking sideways into this alternate set of events.