Amazing that this got no replies so long ago... I have this exact same problem now. Most games are fine, but a handful have very bad stuttering audio.
The thing is, they ONLY stutter when launched from BigBox. If I launch directly from MAME, or even LaunchBox, they play absolutely fine. It's only BigBox causing the issue.
EDIT: I have narrowed it down to the Banner Box theme. Other themes let me play these games without audio issues. My PC is fine to run the theme, I really went overboard with the specs so that I could run modern fighters like Street Fighter V and Injustice, so I know my hardware isn't the problem.