I know this isn't the answer you want to hear, but there is no way to stop this, regardless of whether you wrote your own flash library to play sound or not.
For everyone who said "it works fine for me!" try resizing or moving your browser window as the poster's demo plays out. You'll hear more than just a subtle amount of delay. This is most noticeable in Firefox and IE, but even Chrome will experience it.
What's worse, if you click and hold the mouse down on the close box for the browser window, the sound completely stops until you release your mouse (you can release it outside of the close box and not actually close the window, FYI).
What is going on here?
It turns out that when you start resizing or moving around the browser window, the browser tries to multi-task the act of changing the window properties with the act of keeping up with the javascript going on in the window. It short-changes the window when it needs to.
When you hold down the mouse over the close box in the browser window, time stops completely. This is what is happening in smaller increments when you are re-sizing or moving the window: time is standing still in the javascript world in small, sporadic chunks (or large chunks, depending on how slow your machine is).
Now, you might say "sure, resizing the browser or holding down the close button makes the browser pause, but normally this wouldn't happen". Unfortunately you would be wrong.
It happens all the time, actually. I've run tests and it turns out that even by leaving the browser window completely still, not touching the mouse, and not touching the keyboard, backgrounds processes on the computer can still cause "hiccups", which means that for brief periods (perhaps as small as a few milliseconds) time is "standing still" in the browser, at completely random intervals outside of your control.
What do I mean by "standing still"? Let's say you have a setInterval() call (this applies to setTimeout also) running every 33 milliseconds (about 30 frames per second). Now, you would expect that after every 33 "real world" milliseconds your function would get called. And most of the time, this is true.
But when "hiccups" start happening, your setInterval call might happen in 43 milliseconds. What happened during the 10 ms? Nothing. Time stood still. Nothing on the browser was being updated. If you had sound playing, it will continue playing, but no NEW sound calls would start playing, because no javascript is being executed at all. If you had 5 setInterval() functions running, they would have all been paused for 10ms at some point.
The only way to tell that "time stood still" is to poll real-world time in your setInterval function callbacks. You'll be able to see that the browser tries to keep up most of the time, but that when you start resizing the window or doing something stressfull, the intervals will be longer than usual, but that all of your code will remain synched up (I'm making games using this technique, so you will see that all your game updates happen in synch, but just get slightly stuttered).
Usually, I should point out, these stutters are completely unnoticeable, and unless you write a function to log real-world time during setInterval times (as I have done in my own testing) you wouldn't even know about it. But it becomes a problem if you try to create some type of repetitive sound (like the beeping in the background of Asteriods) using repetitive play() calls.
My suggestion? If you have a sound that you know will loop, give it a long duration, maybe 10 seconds, and you'll be less likely to notice the hiccups (now, the graphics on the screen could still hiccup, but you're screwed there).
If you are writing a game and having the main character fire off a machine gun, don't do 10 rapid-succession calls to playSound('singleShot'), do one call to playSound('machineGunFire10Rounds'), or something along those lines.
You'll have to do some trickery to get around it, but in most cases you'll be alright.
It seems that Flash applets run in a process that is somehow less affected this whole "time freezing" thing going on in the regular browser/javascript environment, but I can still get it to happen, even on your link to the ToneMatrix example, by resizing or moving the browser window.
But Flash still seems much better than javascript. When I leave the browser alone I'd be willing to bet that Flash is not freezing for any amount of time and that intervals are always running on time.
tl;dr:
- you're screwed in what you're hoping to achieve
- try to deal with it using some workarounds
- re-write your project in pure flash (no javascript)
- wait for browsers to get better (Firefox 4 is getting a new javascript engine called JaegerMonkey which will be interesting to watch)
- how do I know all this? I've done a lot of testing & logging with javascript, setInterval, and soundManager/html5 audio calls