This is a IE6 thing with the way controls are losed and run.  MS will either have to unpatch (not likely) or Macromedia will have to release a patch for either the player or the program its self I'm not sure which. 

I'm pretty sure Macromedia (Adobe) has released something already but you might have to recompile your Flash menu or require your users download a newer version of the player.

I found a relatively easy way to deal with the flash problem:

There's an online code generator at Kirupa.com that allows you to input your filename and size, then it generates code to replace the object/embed tags in the .ascx file.

You still have to edit the code to add <%= SkinPath %> to both paths, download the javascript and put it in the same directory as the skin.

An example:

<script type="text/javascript" src="<%= SkinPath %>flashobject.js"></script>

<div id="flashcontent" style="width: 770px; height: 66px"></div>

<script type="text/javascript">
var fo = new FlashObject("<%= SkinPath %>headerflash.swf ", "animationName", "770", "66", "6", "#FFFFFF");
fo.addParam("allowScriptAccess", "sameDomain");
fo.addParam("quality", "high");
fo.addParam("scale", "noscale");
fo.addParam("loop", "false");
fo.write("flashcontent");
</script>

HTH