If cPanel is displaying the wrong version of MySQL, you'll need to access the filesystem for that particular user and remove/rename a file or two.

1. If cPanel is displaying the wrong version of MySQL, you'll need to:

   cd /home/cpanelusername/.cpanel/datastore

   Once in the directory, you should see a file that's named something along the lines of:

   usr_sbin_mysqld_.

2. Just in case something blows up, go ahead and rename the file:

   mv -v _usr_sbin_mysqld_--version _usr_sbin_mysqld_--version.bad

3. Once that's done, login to cPanel for that particular customer and the file will get re-created with the correct info