Vaelen, the schmoe who gives you the quest in the first place, is now in the habit of deleting the quest and your quest items when you talk to him. Now, this isn't right by any stretch of the imagination. Vrakhris mentioned in the forum post that Blizz knows about the problem, and are working on fixing it in an upcoming patch. Meanwhile, there's a workaround to tide us over.
Check this out:
"Basically what is happening is when the instance resets Vaelan will forget that he has ever spoken to you. In order to get around this you will need to acquire another Unadorned Seal of Ascension. Once you have the Unadorned Seal of Ascension speak with Vaelan, he will examine your Unadorned Seal of Ascension and continue his dialog as if you had never been there before.
Once he runs through his starting dialog he will offer you the quest that you should be on, since you have already completed the first Seal of Ascension quest he will give you the second one as well as Vaelan's Gift which will have the Unfired Seal of Ascension and the Orb of Draconic Energy in it.
Complete the quest and return to him, again if you had left the instance long enough for it to reset you will need to speak with him while a Unadorned Seal of Ascension is in your inventory."
Confused as to how this could possibly happen to a quest almost two years' old? Yeah, me too. In any case, I will do my best to make sure my gems don't disappear when I turn in my key. As irritated as I am that the quest is broken, I am glad they've given us at least one way to get around it.