We have already answered to this question in the support thread opened. For a community reference I will paste the answer here as well:
I believe that the reason your users fail to upload is due to the web.config configuration, not because of the ASP.NET FileUpload. The ASP.NET FileUpload, as well as RadUpload, are based on the html <input type='file' /> element, which in turn has been used for file uploads since the advent of the web. The issue that your users face is a timeout issue I believe. If they are uploading from a slow connection the server might timeout the request. Hence, the upload will fail. In order to workaround that, please consider setting higher value to the executionTimeout element in the <httpRuntime /> section of the web.config. For details, please take a look at the following blog post.
the Telerik team