When AjaxFileUpload post back it takes your page URL and appends onto the end of it it's own query strings (contextkey and guid). This works fine if your page URL doesn't already contain any query strings but if it does then you end up with a URL that contains two question marks which then corrupts your own final query string value and this in turn stops the upload from working.
Comments: The work around that I have found is to override the javascript 'AjaxFileUpload.js' file with a static one that has a tiny change to it. The change is to check to see if 'this._postbackUrl' contains a '?' and if so add an '&' rather than the '?' to the querystring as it is appended. Unfortunately I can't log in to codeplex from work so this is from memory, if you search for '?context' it'll show up. Hope that helps.
Comments: The work around that I have found is to override the javascript 'AjaxFileUpload.js' file with a static one that has a tiny change to it. The change is to check to see if 'this._postbackUrl' contains a '?' and if so add an '&' rather than the '?' to the querystring as it is appended. Unfortunately I can't log in to codeplex from work so this is from memory, if you search for '?context' it'll show up. Hope that helps.