There is a problem here, I've just confirmed it on my server.
If I have WHM > Server Configuration > Tweak Settings, System Tab,
Accounts that can access a cPanel user account
Set to: cPanel User only
Using HTTP Authentication, then User root using root password to login to cPanel gets Login Attempt failed message.
If I disable HTTP Authentication and login to cPanel as root with root password I get internal server error. See attachment.
monarobase, you might want to open a report on this and link them to this thread.
http://go.cpanel.net/bugs