There are a few items you need to make sure are done correctly in order for flash ExternalInterface to work correctly in IE:

1. The object tag needs to have the correct clsid attached
2. If flash is loaded dynamically in the page as opposed to being written in the initial html, the object tag must have an id.
3. In order to access javascript with same permissions as you would have the js code directly in the page, you need to have . make sure allowscriptaccess is written just like that with no capital letters