You should check whether root is permitted to login remotely using SSH, this is configured in the /etc/ssh/sshd_config
file. You can either use the cpanel File Manager to open the file and edit the directives, or login to SSH as a local user and then change to the root
user with the su -
command.
From the console the commands to check is;
# grep -i Root /etc/ssh/sshd_config
#PermitRootLogin yes
# the setting of "PermitRootLogin without-password".
PermitRootLogin yes
If you need to Change PermitRootLogin yes
then you will also have to restart the sshd service.
Also, it is not clear that the users for WHM and local user accounts are using the same password database. According to the cpanel docs it looks like the root
user to login to WHM is also the system root
user - http://docs.cpanel.net/twiki/bin/view/AllDocumentation/CpanelDocs/Glossary#QqR
So it would seem that the problem use due to PermitRootLogin no