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Have you resolved this issue? I just setup a Raspi 2 model B with RetroPi 3.0 BETA. Everything was working fine. I had sound coming from the emulators, but the controller config needed to be done. After i edited the retroarch.cfg file and rebooted, the video looked zoomed in, and the audio no longer worked.

I had this problem with previous versions of RetroPie. I found some info about adding in audio commands and will be testing until i find the solution.