This is an old issue on the Dolphin Wiki.
When loading up Navi Trackers (4 player party mode) VBA-M will constantly emit garbage audio. It is loud, and makes recording footage pretty impossible (I was going to record footage for Dolphin's wiki)
mGBA supposedly works properly according to endrift, Higan plays no audio whatsoever. Endrift actually should know what the problem is, so if you ask her about this she should be able to give a huge hint as to what is wrong.
I verified this in the latest GIT of VBA-M as of this date. The audio sounds like a very loud humming noise. It drowns out Dolphin completely.