First of all, I’m not entirely sure if this is a bug or if I’m misunderstanding how runes work. I was under the impression that you added runes to armor pieces, and for each identical rune, you gained another effect, up to 6/6 possible effects. So imagine my surprise when I noticed mine was sitting at 12/6.
I took all my armor off, and when I did that, it claimed 6/6 when I hovered over each piece that wasn’t on my character. Put one back on, it went to 7/6, and so forth until all pieces were back on and I was at 12/6 again.
Out of curiosity, I put two cheap minor runes on some junk armor, and they behave as I expected, giving 0/2 when not worn and 2/2 when worn.
It would appear that the game seems to think I already have all 6 runes on even when I’m not wearing anything. I attached a couple screenshots, showing the same armor piece with all armor on and all armor off.
