Not sure if this is a bug yet. When you loot a quest item from an elite in WoD, it will not show that it is a quest item ("!" over the icon) until you mouse over it.

So not sure if this is with bagnon or not because I haven't tested it without bagnon enabled.

Also on a side note, I have seen this and people are reporting that if you click on an item in the loot won display (toast like annoyance that happaens over hte action bar), it opens the default bag with the default interface and you can't close it unless you reload the ui.

Yeah, reasonable the icon should show even if it is flashing as a new item. Fixed.