I had this problem today as well. I just replaced both the swfupload.js and the swfupload.swf files with the ones from the newest SWFUpload v2.0.2.Release.zip file at http://www.swfupload.org/node/1/release . I used the swfupload_f9.swf file from the archive. My uploads are working now. I'm still testing and I'll post again if I have problems but so far so good.
Hope this helps.