It is because of Form's encType attribute.
you need to set
encType = "multipart/form-data"
Try this code inside Init evet of your control. It will add the encType attribute to the form you have on your page and then you may receive file bytes inside FileUpload Control.
ScriptManager.RegisterStartupScript(page, page.GetType(), Guid.NewGuid().ToString() + new Random().ToString().Replace(".", ""), "$('#yourFormID').attr('enctype', 'multipart/form-data');", true);
Note: you need to have JQuery referenced onto your page or alternatively use javascript to do this job.
Good luck :)