Isn't one of Zetsu's specialties making it's chakra signature resemble whomever it wants. I'm assuming that Obito was wrapped in that Zetsu clone during the kyuubi attack on Konoha, hence concealing Obito's chakra signature, and possibly giving off Madara's. We've seen how the Zetsu clones can mask anyone's chakra signature and fool the sensor corps.
The thing is, we only saw Zetsu copying others' chakra while impersonating them and it's unknown if they can hide others' chakra, so I wouldn't bet on that scenario. I only mentioned that Zetsu cloak could mess the chakra signature in the eventuality of the older Zetsu still not having the chakra hiding feature.