Apparently Agori and Matoran speak in different languages. Miraculously, the bio-mechanical beings of the MU were able to access a latent ability to speak Agori once they stepped out of the robot (though for whatever reason, our Reign of Shadows group - Lewa, Helryx, Vezon, etc. - cannot).
What confuddles me is the fact that the Great Beings apparently speak in the programming language they designed for the Matoran. In the serial Brothers in Arms, the Great Beings have a chat with Mazeka - in programming language, because that's what Matoran speak.
But wait, you might say. Don't forget Matoran can speak Agori once they leave the robot!
Yeah, but what about the RoS group?
Hold on! you reply. They speak to a Great Being too! That means the Reign of Shadows group must be speaking in Agori too!
Nope, sorry! According to the 'Farshtey Feed', Greg said this:
With Mata Nui dormant, Lewa Nuva will likely have to learn the Agori language on his own.
I assume this means that everyone in the RoS group will have to learn an entire new language; I can see no reason why it's just Lewa.
Either Greg is trying to make this all an elaborate plot point, or he just forgot that Agori and Matoran have different languages when he was writing those serial scenes. Or the Great Beings sit around talking in their own programming language to each other. Like a secret code.