The last version of my flash multiple upload script would spawn an alert box containing the message “A script in this movie is causing Flash Player to run slowly” after the script had been open for 15 seconds. Even if the user chooses to let the script run, the window will pop up again every 15 seconds.

This obviously is a huge problem, as many users will unknowingly abort the script. You can Read More about the issue through Adobe’s Technotes.
The fix was to add a dummy onEnterFrame event which refreshes the timer. I have updated my code here
The only update was to change how I initialized the movie in multipleUpload.fla, and to attach the onEnterFrame event handler.
import com.vixiom.utils.MultipleUpload
System.security.allowDomain ("*.localhost.com");
var uploadMovie = null;
_root.onEnterFrame = function() {
if (this.getBytesLoaded() / this.getBytesTotal() > 0.99) {
uploadMovie = new MultipleUpload (this.files_dg, this.browse_btn, this.upload_btn, this.cancel_btn, _root.object_type, _root.object_id, _root.token);
_root.onEnterFrame = function() {
trace ("onEnterFrame called");
};
}
};