Did Zetsu know about Tobi's truth/identity all the time?
Zetsu did know Tobi from the beginning.


   Tobi has interacted with the White Zetsu the moment he arrived to Madara's cave. Black Zetsu was created by Madara in Obito's presence.


The reason for Zetsu supposedly not knowing Tobi could be


He wanted to keep it hidden from the other Akatsuki members.
Kishimoto haven't thought about it at the time.