I have the same issue with my warlock. My guess is that it's because you're using a new shader. I've been using the "blighted chalice" shader you can buy from Eva Lavante ( the guardian outfitter ) and that shows up as "classified" in the inventory of both the destiny companion app as well as the destiny loadouts app i use. Just give it time, once there's some kind of app update im sure it'll be fixed.