You should search for those Job Stones in your Inventory, in your Retainers, Saddle Bag and your Mails. It is not possible to drop, discard, sell those Stones. Try to equip a Reaper Weapon or a Blue Mage Weapon and see if it helps. I had now and then my Job Stones too hidden in my Inventory, don't know why, it just happens now and then. Check your Blue Mage Book, are all Spells still there, is your Gear still in your Armory / Inventory? Then your Stones should be somewhere and go to the NPC's where you took the Job Quests and see if they have a Quest.