Unfortunately the above link is broken. However I've used php and flash together before. I found a tutorial vid on youtube that should be a good substitute for the above missing tutorial: http://www.youtube.com/watch?v=_OGrvlCqttU
The first php upload progress bar I ever used had to actually use perl to do the dynamic progress updates. Since then any multiple file upload tools with progress bars that I've used in php have always been tied in with flash for their dynamic aspects. These seem to work smooth and seamlessly.