As far as I know there should be no difference using <asp:FileUpload in a UserControl vs a Page. Maybe you don't have the events wired up correctly in the usercontrol. Best to set a break point and step through your code and see what is happening and if events are firing as expected.
You might want to consider using NeatUpload as we do in existing features, you could study the code for Shared Files or ImageGallery for examples of uploading files.
Hope it helps,