Yes, it can be the rotors. Some rotors will actually change dimensions slightly when they get really hot. If the thickness variation becomes too great, it feels just like warped rotors. Rotors that are not quite true to begin with can be more sensitive to changes when they get hot. It is aslo possible that the rotor is not propely seated to the hub. Make sure that all rust in the mating surface between the hub and rotor is removed. Use a little anti-sieze if needed to keep it from rusting in the future.
You could also have sticking caliper slide pins or inadequately lubricated calipers.
