I was working with a B+ and had a ton of audio issues, sounds like what you are describing. In my case I was just running MAME4ALL and it all had to do with how hard the CPU was working. I was trying to do a vertical in setup which requires the Pi to do extra emulation for the screen rotation. This seemed to cause the audio to breakup. First switch I made was to use a USB audio card, to all it to do the audio processing. I got that all working well, then I switched monitors and the audio issue was back again. As it would turn out, I wasn't running the monitor at it's native resolution, which required more CPU power, manifesting it poor audio. If I ran the monitor in it's native resolution, wall was fine. Audio problems varied by games, but for me I found that Donkey Kong was the worst, so that was my test game. Once I got things setup so that Donkey Kong worked, everything else was fine.

Hopefully this is helpful to you.