I know this is a known issue but have been checking into it with the following results.
Had a quest the required xx of xx mobs killed.
(Strike Them Down)
http://www.wowhead.com/quest=46246/strike-them-down
The quest watch was not updating after a NPC kill. Found out that the Quest_Log_Update was not registered and put the following on line 5467 of NxQuest.lua
CarboniteQuest:RegisterEvent("QUEST_LOG_UPDATE", "OnQuestUpdate");
After I put this in the quest log updated on each kill for the quest but I see a reduction of framerate mostly in some instances like Skyhold. Still have not worked that out but will keep looking..