For those running into problems with mp3 playback, it seems the issue is 48kHz sample rates and a change in Flash. For details see https://www.blackcj.com/blog/2009/01/30/flash-player-10-48khz-sound-playback-bug/
I don’t immediately see how to patch the source code with this fix, but it’s 3AM and I need some sleep. For now I’m having to not use the plugin rather than re-encode all my mp3s I want to embed.
Here’s hoping the original author will patch his code someday.