I just moved from Recalbox to Batocera and I am havong the same issue.
Every time I boot up Batocera there is no sound until I change both sound output options. After this I can change back to “auto” and the sound continues fine until the next boot.
I am using HDMI 1 as the HDMI 0 did not work properly on Recalbox, but now I have two questions:
1 - If I star using HDMI 0 the issue might be solved?
2 - Is there a way to keep Batocera from change the sound output options at every boot?