I'm having a similar issue, but the javascript I'm calling
within Flash is the show/hide layer js from Dreamweaver. It works
fine inside FF, but the same behavior has no effect in IE6/7. And I
couldn't get my swf/js to integrate exporting as a Flash 8 movie on
either the desktop or the server. I had to downgrade to Flash 7 to
get it working at all inside FF and Safari.
Here's a link to see it in action (only Carroll and Troup
counties are active);
http://pixegen.com/sandbox/map.html
Any ideas on why IE isn't working?