When I download submitted uploads, I do not receive all of the downloads

Do you mean to say that there are download links that are not working? If yes, please share us the links here so we can check. This thread is now private so you are safe to post the links here.

For downloading the file uploads at once, we have this workaround:

http://www.jotform.com/help/315-Downloading-File-Uploads-in-the-form-using-DownThemAll-Mozilla-Firefox-Extension

Thanks