I have been in four quests with empty Primeval Obelisks. No runes.
The ones I've encountered seem fine. If these are commonly done lower level quests its possible that they havent respawned from the last person.
This happens often in lowlvl quests.
They respawn on a timer. So, every 10-15 minutes, they reappear.
This just means someone did the quest just before you and took all the runes.
They are indeed on a refresh timer.