Using SWFUpload v2.2, Firefox 3, IE 8, Flash 10 In my ASP.NET application all uploads are being processed by upload.aspx (I have the correct upload_url set in the settings o
It sounds like you could be running into this Flash bug. Nort's solution is the way most people have been working around it. Depending on your language/framework however, you may need to add some additional server-side code to take the session variable from the url and force it to be used as the current session.
You can try the solution in this StackOverflow question, or try googling something like 'flash upload cookie'.