While you are flatfooted, are you denied your dexterity bonus to reflex saves?
Assuming you are, if Caster casts fireball, you fail to identify it with spellcraft, are you then flatfooted against it? You don't have any reason to know it's a fireball so getting less damage from it due to quick reactions (dex bonus) shouldn't apply, but you know the opponent is there so you shouldn't be flatfooted against things they do unless they feint.