We've seen that chakra can get split off and still retain its "character" (like how the stupid Brothers and Tobi got Kyuubi chakra). So what if Tobi is a piece of Madara's chakra he left behind in case he was killed? Maybe it even "possessed" an Uchiha, like an untamed bijuu would.
In this case, the resurrected Madara might have known who Tobi is, but it would have been pointless for him to say. Tobi has been "alive" and knows more about current events than the resurrected Madara, has a plan, etc.
This case would explain why the Kyuubi said he was under Madara's control, why Tobi has called himself Madara, why Tobi hates the Uchiha, how he awakened a Rinnegan, how he is still alive -- switching bodies by possessing people, kind of like Orochimaru, etc.