Nevermind. It was a kodi setting not LE. In case someone else has the same issue I diffed guisettings.xml and found these to fix the problem:
Code
<setting id="audiooutput.dtspassthrough">false</setting>
<setting id="audiooutput.eac3passthrough">false</setting>
<setting id="audiooutput.passthrough">false</setting>
<setting id="videoplayer.adjustrefreshrate" default="true">1</setting>
<setting id="videoplayer.usedisplayasclock" default="true">true</setting>