I think you are confusing the database prefix with the table prefixes. One has nothing to do with the other, literally. For example, I've set my server to add the subdomain prefix to the database name so that I will know what site the database belongs to, like campus_moodle. The tables within this database are prefixed as specified in the config.php with 'mdl_'.
I wish folks, would at least, take the time to learn the OS and database of their choice; before venturing off to install web-based apps. Some beginner PHP/MYSQL/APACHE/LINUX primers would not be a bad thing. You must have a local geek or 13 year old whizkid in your neighborhood. Sorry for the rant.