The part of that Rune Caster hidden class quest where you talk to the Chronomancer Master in Stele Road and she tells you she is looking for the stone and to come back later is currently bugged.
If you do not wait inside Stele Road next to the Chronomancer Master NPC - the timer (hidden timer, an addon can reveal it) will never end, every time you come back to her, the timer will be 2 to 3 hours long and never runs out unless you stay there.
So for myself I placed my character there, online, this morning and came back home and the timer was gone and I got my last Rune Stone.
This is the temporary solution until the bug is properly fixed.