I'm having the EXACT same problem. I had some preorder codes for a helmet and armor, and its not showing up! Every time I level up it lists that I have the helmet (deadeye) yet its never in my inventory and I can't select it. Whats going on???
I also noticed that if I launch Waypoint from Halo 4, my console locks up and I have to do a hard reset. Waypoint loads fine if I load it directly. I don't know if these issues are related.