So I bought 6x Superior Runes of the Necromancer to put on my level 60 gear for my necromancer, and I wasn’t getting any of the set bonuses at all. It was showing me as having 12/6 on the set. Someone said it was counting my PvP gear, and I didn’t even know I had PvP gear since I never do any PvP at all. So I headed to the Heart of the Mists, unequiped all the gear in there, came back out of the mists, and my set bonus on my PvE gear activated. Because I didn’t want to store that PvP stuff, I destroyed all my PvP gear.
So apparently there is a bug where the game thinks I was wearing 2 sets of those runes and would not give me the bonus, not until I unequiped my PvP gear in the Mists.