#3 - Sept. 18, 2012, 6:59 p.m.
Thanks for reporting this! There are actually 2 display issues here:
One is that the item UI displays rune set bonuses as cumulative across both the player’s PvE and PvP equipment (thus why it shows 12/6 instead of 6/6). However, the attribute bonuses themselves are applied based on how many runes are equipped to your currently equipped armor set, so while it may look incorrect, your character should have the correct attribute bonuses from both sets.
The other issue is that attribute bonuses from newly equipped runes do not display on your Hero panel if you’re under the effects of Level Scaling. So for example, if you are a level 80 and equip the 2 piece bonus for Superior Rune of the Undead while in Wayfarer Foothills, you won’t see the +15 increase to your un-scaled Toughness attribute on your hero panel until you change maps. If you did the same thing in Hoelbrak however, the Toughness increase would be displayed as you equipped the rune.
TL;DR: Fear not, you can use the same rune set in PvE and PvP without missing out on any attribute bonuses – it just currently displays incorrectly.