I recently updated my WHM and observed that mail headers included in my case X-PHP-Script, X-Source, X-Source-Args, X-Source-Dir For me is very important to hide these values since i don't want my users to know my admin link. I fixed my problem by: 1 - Rename etc/eximmailtrap to anything else using WinsCP or SSH Because exim checks if file eximmailtrap exists and adds the headers. 2- Recompile Apache and remove from Exhaustive Options list > "MailHeaders" These seems to fix the security problem.
Well this was not a question, only and advice to prevent hackers to find your admin panel or source of your scripts.
Email headers are showing your X-PHP-Script link because Mailheaders php modules is installed on your server. If you want to remove your link from mail then you need to uninstall Mailheaders modules from your server through easyapache.