Maybe the way I was asking was confusing.
I want my files to include the AC_RunActiveContent.js file when I publish. I am using CS4 and it is not automaticly including that AC_RunActiveContent.js file.
What do I have to do to get it.
Just go and change the publish settings from file menu and publish your file.
AC_RunActiveContent.js is not created anymore in CS4 because it is obsolete. It was used as a workaround for IE6 and earlier versions but will no longer usurp a users security settings in IE8. It is not required for IE7 and succeeding versions. SWFObject is now the defacto method for embedding Flash. You can get those files and instructions at http://code.google.com/p/swfobject/, but it does not override local security settings.