Symptoms
In WHM under "Basic WebHost Manager® Setup" the shared IP is configured but when creating an account another IP is being used as the sites IP.
Description
This is something that would have been administratively put in place as the/var/cpanel/mainips/$user files are typically used for resellers. In the case for root if /var/cpanel/mainips/root exists with an IP that IP will override the shared IP setting in WHM.
Workaround
All that needs to be done is remove /var/cpanel/mainips/root from the server and then new accounts created as user root will use the shared IP configured in WHM.