This is for Chrome (latest versions always), as it seems to have the best support for HTML5 audio right now.
First, click on the audio plugin in the project folder window. Make sure on the left that audio timescale is turned on.
Also, it seems to depend on which folder you use for audio. If you put it in the "music" folder, then audio will pause correctly when timescale is "0". If audio is in the "sounds" folder, this doesn't work for some reason.
If you tell any audio to stop when a certain button is pressed (e.g. On Keyboard Button 'A' pressed, Stop audio), that should work. It works just fine for me. If you tell it to mute (like for looping ambient sounds), that should work too.
Like I said, make sure you have the audio timescale turned on. Play around with the 2 different settings ("sounds" and "sounds and music").
In Chrome I've managed to get most things to work properly.