Try to use this when you close the popup window.
document.getElementById("MediaPlayers").stop();
Or you can use another div to wrap this player, and then add your html into innerHTML when open popup window and then remove all when you close the window. like
<div id="playerWrap">
<OBJECT ID="MediaPlayers" ....
.....
</OBJECT>
</div>
javascript code:
document.getElementById("palyerWrap").innerHTML = "";
reference by http://www.htmlforums.com/multimedia-elements/t-accessing-mediaplayer-functionality-from-javascript-65899.html