I'm afraid I don't know enough about how ajax4jsf works to really help, but one thing I might suggest is that the requests are being intercepted by the MultipartFilter.
Anyone have a work around for this? I am getting the same problem.
I'm pretty sure that you won't be able to do this with ajax4jsf as it is now.
You should probably ask on the richfaces forum and especially the thread on rich:fileupload (http://www.jboss.com/index.html?module=bb&op=viewtopic&t=119282)