Technically MailScanner should be able to use cPanel's ClamAV connector and you shouldn't need a separate ClamAV installation. This is noted on ConfigServer's site as well here: Installing ClamAV with MailScanner
Thanks for all answers.
We decided to remove the older version with yum and in doing so we realised where the older version came from, dependencies to also be removed included imunify-antivirus which we tested and thought we had removed. I guess it installed an extra version of clamav.
Please mark 'Solved'