Check if your report's QWeb template references the external_layout_header. This is often done like this:

<t t-call="web.external_layout">

    <div class="page">

    </div>

</t>

Being as you have wkhtmltopdf installed and you can see the PDF even though its not displaying properly it requires that the web.base.url has a valid certificate for it to generate the report correctly, if for some reason this is ignored then the Headers and Footers will be deformed. 

To get them to display the way you want, activate developer mode, Technical >> System Parameters search for url, you will see only web.base.url along with your domain name unless you are using localhost:8069 then the pdf would work. But for a FQDN the report will not show the footer as wkhtmltopdf is most probably behind a proxy in which case create a new system parameter called report.url  and set the value to either http://localhost:8069 or the docker container name if using Docker. So it would be http://<container_name>:8069 or which ever port you are using.

There is no requirement to restart Odoo, just take a look at the report and see if the footer shows. 

** You may need to fix the Paper Format margins, Technical >> Reporting >> Paper Format and set up the xlms to your requirements, but I found this to work a treat as it forces wkhtmltopdf to use report url rather than the external facing one.

Hope this helps those who are having this problem. 

Hello  Christopher,

You can temporarily switch from PDF to HTML generation to verify if the header is displaying correctly. Another troubleshooting method is to open the generated PDF using a PDF editor (such as the free PDFGear) to determine whether the logo is extending beyond the page boundaries or if it's not being generated at all. 
Hope these can help you.