This is HDMI "handshaking" which involves the receiver and tv as well. Typically you can't do anything and it's not related to the Chromebox per se.
It bitstreams without issue including 5.1...
Well, as if I needed another excuse to get a new TV. I have never had any handshake issues with this setup and other sources (Xbox 360, FireTV, Dune, Mede8er, etc.).