clearing the list is just client side operation with list. It doesn't resets the FU to make new files uploads available(as actually old one is on server).
http://livedemo.exadel.com/richfaces-demo/richfaces/fileUpload.jsf - sample shows list cleaning with the button. sources at http://jboss.org/richfaces/demos.
If you want to use just built in control - use a4j:support for onclear event and reRender the FU.