They will be on the wrong runes. If you get it right, you should get a cutscene and the door in the floor will be unlocked. Without giving too many spoilers double check the clues you got by 'using' the 5 items you got for the quest e.g the engineer's sword, maxos bracelet etc.
There are 5 orbs but about 8 runes; you just need to put the correct orbs on the correct runes and leave the other incorrect runes with nothing on them.
