Madara was resurrected in the state of when he was in his prime. I think just after Hashirama's fight because it is stated that he awoke the Rinnegan then. The reason why he was resurrected with his original eyes is because that's what the Edo Tensei does. It resurrects you in the state you were in when you last died. But Madara's state was an exception because of what Kabuto said. Remember, Itachi also had his eyes but Sasuke actually has them in the form of EMS.
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