At first I tried using a single embed object, then changing the src of the embed on a button click and using embedObj.Play(); but for some reason changing the source of the file stopped that happening.
My second idea was to replace the entire embed code each time, and then call Play on the embed to get it to play. Still no luck!
Finally after a bit of searching I found somebody that had managed to do it. Its similar to my second idea only instead of calling .Play() on the embed object you just use
autostart=true in the embed code, simple!