PROBLEM SOLVED
I ran a scan on https://www.unmaskparasites.com/
It listed a script pointing to testedom.tk/traffic.js and it seemed suspicious so I searched my header.php and index.php files again.
Hidden inside my Header.php file was this script and apparently it has been causing the problem.
<script type="text/javascript" src="https://testedom.tk/traffic.js">
Deleted the script and the pop-unders are gone. Now lets hope they don’t come back.