Can I have the PDF that is returned to me have the company logo?

If you are talking about PDF files of your submissions, yes. You can show headers, text, and images in your downloaded PDF submissions, by following our guide:

http://www.jotform.com/help/305-How-to-include-Headers-Texts-and-Images-in-the-PDF-format-of-a-submission.

As described in the guide, all you need to do is go to Submissions page of the form where you wish to enable this, click on the little gear-shaped icon on the right, and select Show Headers and Texts option.

Please let us know if you need further assistance.

I have that selected and I am not getting it when I receive the submitted form.

Enabling that option will only take effect on the newly downloaded PDF onward. 

Another solution is to edit the submissions PDF and add your logo in it.

Here's how:

Go to your form submissions page > click on Get PDF and click Customize PDF.

You will be redirected to the PDF editor after that.

Thanks!