If you're using the upload manager to upload your files then you need to make sure that the complete transfer is performed. If you lose the connection or close the browser the file will not be saved.
A better way to upload is using the FTP method. If you go to the media manager page you will see instructions to drag-and-drop files directly into your FTP account using Internet Explorer.
You can also use Video Caster to directly upload and publish your files to Video Desk. You can learn more about Video Caster from the following link:
http://www.deskshare.com/download_details.aspx?ID=2