Q: Thunderbolt to HDMI cable messes with audio sync

I used to have a laptop which I plugged into a Sony Bravia via HDMI which gave audio output through HDMI to a Sony Home Theater System.

Since getting a MAC, and using thunderbolt-HDMI, the audio sync is all messed up. Usually one remote (TV) can control all channels/audio/inputs, but as soon as the thunderbolt is plugged in this all stops and I have to use seperate remotes.

Has anyone come across this before? Thanks