Hmm.
But Nagato's eyes could have been Madara's if you think about it.
Tobi said he gave Nagato the Rinnegan. BUT Tobi is also a lair. "I am Madara!"
But, on the other hand... What it were true, since Madara wanted to us Nagato to resurrect him with the Rinnegan, Madara could have given the eyes to Tobi to give to Nagato. So maybe those Rinnegan eyes are just Madara's all along.