It seems the flash multi file upload does not work behind a proxy. As found on the YUI upload pages as well:
Because of Flash limitations, the uploader behavior when working through a proxy server is inconsistent and unreliable.
There are some other also interesting statements:
Because of Flash limitations, the uploader does not support basic authentication.
When uploading to HTTPS servers, be aware that Flash does not support self-signed certificates. You would need to obtain certificates from a recognized certificate authority.
It would be good to put these on the hippo documentation website, because this means people might run into these problems while installing on their servers.
See http://developer.yahoo.com/yui/uploader/ for more information.