Try looking for an swf file uploader. These are flash based uploaders that will upload the file, and on completion, usually does a form submit and from there you can get php to finish processing the file (moving, renaming, whatever).
I've used these in the past to get around this. I don't have a specific one as an example, but if you google for it, you'll find them.
Also, depending on how the server is configured, sometimes the php settings can be overwritten using htaccess or php.ini files.