I found the tome of fire in the serpent temple, in the undertemple treasury, that's the room with a gate that needs the skull key just past the place where you kill the naga. You don't get the skull key until later so you may have forgotten to go back.
The tome of water should be in the sunken city in the lost sea and the tome of earth is in Cet's pyramid in the isle of sands.
I'm not so sure that the special objects are placed randomly, in my games they seem to be pretty much in the same place as reported by others.
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