I am trying to call a Actionscript function from javascript but I am having problems in Internet Explorer. I am using Swiff.remote in mootools 1.2.1 to call the actionscript fun
Maybe this can help you out, looks like a similar problem but using the swfobject.
http://blog.deconcept.com/swfobject/forum/discussion/1064/swfobject-21-problems-with-externalinterface-in-ie/
Good luck.