Are you using HDMI video+audio, or HDMI video+analog audio, or analog video+audio? If spdif is involved then things can get more complicated.
The sound of intro video will be played on all audio output devices, but after you get into EmulationStation the a-out device will be auto-recognized by PulseAudio and only one of them will be used.
So I guess there’s something wrong in figuring out which audio output device should be used.
You can manually set the audio output device, by press start in the main menu, then choose EmuELEC Setting->Audio device. Change it from auto to the one that works for you, reboot to verify. E.g. Analog aout is usually “0.1”, but since you have audio issues I think the number might be different from ordinary Amlogic devices and you have to try each of them.