Further research:
A few tickets are on the forums:
HomeAssistant AIO HDMI CEC error (clean install) (mine)
All in one on a Rapsberry PI 3 fails (This goes back to March)
https://github.com/home-assistant/fabric-home-assistant/issues/47 (This was closed because it was successful on jessie lite but a poster later said they also get this issue.
https://github.com/home-assistant/fabric-home-assistant/issues/55 (This finds the cause and lists the next steps to take, however libcec itself is still broken for Raspberry pi at time of writting)
Libcec research:
https://github.com/Pulse-Eight/libcec/issues/362#issuecomment-317258888 the issue tracker of the libcec fault
https://github.com/Pulse-Eight/libcec/commit/5b4faecdeb1d6f8b27822fc50f4b49f6f5c66b95#diff-b81d8c50f4b84adb2a4bb9138dbbf2d3 (The file that is commiting the break in libcec)
So for those with this issue - it is not HomeAssistant at fault, but libcec. I don’t know if following that issue and updating will resolve the issue, I’ll probably just start from scratch to be sure 