I've had this exact same problem for about four months now. I even finally called a gm, he had me get all 6-7 sets of af I had in storage npc out and toss it. However, that didn't fix the problem, and he also wouldn't/couldn't give it back to me. Redoing that much AF is alot of work, plus I still couldn't reset the quests to redo it anyway, so I called a SGM. Basically told sorry, I can see what the problem is, but I'm unable to give ingame hints, you're sol. Never got my af back, and am unable to do af+1 anymore
All af quests are under the completed side of the quest log. However, somewhere, something isn't flagged completed.