The only time they should stop working is if you enter the castle without one in your inventory. An imp shows up at that point and 'borrows' your teleporter stones if you have one or both with you. If not, either the imp shows up the next time you try to use one, or they stop working until the point he would have returned them (in the council hall).
If you drop both teleporter stones on the ground can you click on them to telelport back and forth? If they should be working, but are not, stick them in a chest and download (or transfer from a previous save) a new set of teleporter stones;
Lost Items - guide and directory of inventory files 
