We tested with ASP.NET 2.0 FileUpload control and it works fine with our Sitefinity project. The "enctype='multipart/form-data'" was rendered in the form tag.
We used the attached user control for our tests.
Please make sure that the form tag is set CmsForm instead of the default HtmlForm in the master page (xxx.master):
<sf1:CmsForm ID="form1" runat="server">
Actually, the FileUpload worked fine with both forms (ASP.NET HtmlForm and Telerik CmsForm). Please try both cases and let us know if there is any difference.
Also you can send us your custom module, so we could investigate it locally.