It can be related to Webfaction configuration (they have nginx proxy, and my app is webpy running under apache2+mod_wsgi) because it works in my dev cherrypy server.
Here are some bits from javascript code I use for upload:
/* Bind drop events */
    $(this).bind({
        "dragover": function(e){
            var dt = e.originalEvent.dataTransfer;
            if(!dt) return;
            if($.browser.webkit) dt.dropEffect = 'copy';
            $(this).addClass("active");
        return false;
        },
        "dragleave": function(e){
            $(this).removeClass("active")
        },
        "dragenter": function(e){return false;},
        "drop": function(e){
            var dt = e.originalEvent.dataTransfer;
            if(!dt&&!dt.files) return;
            $(this).removeClass("active")
            var files = dt.files;
            for (var i = 0; i < files.length; i++) {
                upload(files[i]);
            }
            return false;
        }
    })
/* Upload function code cut down to the basic  */
function upload(file) {
    var xhr = new XMLHttpRequest();
    var xhr_upload = xhr.upload;
    xhr_upload.addEventListener("progress", function(e){
        if( e.lengthComputable ) {
            var p = Math.round(e.loaded * 100 / e.total );
            if(e.loaded == e.total){
              console.log( e );
            }
        }
    }, false);
    xhr_upload.addEventListener( "load", function( e ){}, false);
    xhr_upload.addEventListener( "error", function( error ) { alert("error: " + error); }, false);
    xhr.open( 'POST', url, true);
    xhr.onreadystatechange = function ( e ) {   };
    xhr.setRequestHeader("Cache-Control", "no-cache");
    xhr.setRequestHeader("X-Requested-With", "XMLHttpRequest");
    xhr.setRequestHeader("Content-Type", file.type);
    xhr.setRequestHeader("X-File-Name", encodeURIComponent(file.fileName));
    xhr.setRequestHeader("X-File-Size", file.fileSize);
    xhr.send(file);
}
If I fill span with percentage value in progress event, then in Safari it goes from 0% to 100%, then from 50% to 100%, and after that upload is done. Chrome and Firefox are OK.
e.loaded == e.total is reached twice per upload, since I see this in my console log:
console log http://img824.imageshack.us/img824/4363/screenshot20110827at101.png
In the first logged event totalSize is equal to the size of file, but in the second it is twice as much.
I would try heavy use of the console to get to the bottom of something like this. Put a console statement at every major piece of code displaying something meaningful each time:
for (var i = 0; i < files.length; i++) 
{
console.log(files[i]+", "+i);    
upload(files[i])
}; 
and then again inslide your upload().
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