Dynamic Flash publishing problem and workflow

I have a recurring problem with publishing AS3 and bringing in dynamic content such as swfs, jpgs, flvs etc. It works when you publish out of Flash (Cntl-Enter). It sometimes works publishing locally in a browser with an HTML file (with the SwfObject 2.0 or the standard CS3 publishing code). Then when I upload it to a server in only works on certain files, but not on others.

As an example, I had a working as3 dynamic driven banner on a web server. I had to change the height and republish it on the server. So all that changed was the stage dimensions in Flash and the height value of the HTML as well as the name being changed on the swf and html. Now it doesn’t work.

Is there a certain workflow for dynamically published Flash on a web server to get past security restrictions. I know about Mime types and Cross Domain Security Files.