I had the same problem, but just adding dummy text back into the player container div wasn't working for me. I ended up unloading the player on the onClose event of the overlay, and immediately after re-inserting some dummy text into that same div:
//when a video icon is clicked
$(".videoIcons a").click(function() {
//get the URL of the video that was clicked
var videoUrl = $(this).attr("href");
//create a variable for the player, passing the container to install it in,
//the location of the player, and a bunch of arguments including layout and url of video
var player = $f("playerContainer", "/flowplayer/flowplayer-3.1.5.swf", {
clip: { url: videoUrl, scaling: 'fit' },
plugins: {
controls: {
sliderColor: '#000000',
volumeSliderGradient: 'none',
sliderGradient: 'none',
durationColor: '#ffffff',
progressGradient: 'medium',
buttonOverColor: '#33597C',
tooltipTextColor: '#ffffff',
tooltipColor: '#5F747C',
timeColor: '#eb0000',
bufferGradient: 'none',
volumeSliderColor: '#000000',
borderRadius: '0px',
buttonColor: '#33597C',
backgroundGradient: 'none',
backgroundColor: '#111F2C',
progressColor: '#FF0920',
bufferColor: '#e6555c',
timeBgColor: '#274560',
height: 24,
opacity: 1.0,
background: "url/images/playerControlBar.gif)"
}
}
});
//open the overlay and install the player in it
OpenOverlay(player);
//stop the link from working (to prevent the video from downloading)
return false;
});
function OpenOverlay(player) {
$("#overlay").overlay({
//create the blue background using the expose plugin
expose: {
color: '#0C2E49',
loadSpeed: 500,
closeSpeed: 800,
opaicty: 0.85
},
//load our player
onLoad: function() {
player.load();
},
// when overlay is closed, delete the player
onClose: function() {
player.unload();
$("#playerContainer").text(" "); //dummy text to make this thing work in IE (sigh)
},
//specify that we want to use overlay programatically (rather than by triggering off a link)
api: true
}).load(); //load the overlay immediately after the construction
}