I installed RetroPie from source last week and I have Genesis, Master System, PSX, SNES, NES, GB, GBC, PC Engine, and Sega CD all working great. They are fast, have sound and the controllers are working great.
GBA is running smoothly and works great with the controller, but there is no sound at all. I tried different sound frequencies in the settings (by pressing F10 in-game).
I have a Raspberry Pi B+ and have it going through HDMI.
Any thoughts?