he was exhausted thats all. all his chakra had been drained and he was dying.
its similar to what happened to sasuke after the Vote fight. his sharingan deactivated and his eye looked like he was going blind but obviously he didn't
It looked like the effect of what happens when you over use the MS... Madara really must have been cocky after he was revived, he should have used inzaghi after his death but he probably thought he'd never be defeated.