If you see this in the mysql log when starting mysql, and can not run upcp;
/usr/sbin/mysqld: /usr/sbin/mysqld: cannot execute binary file
140513 00:16:10 mysqld_safe mysqld from pid file /var/lib/mysql/<hostname>.pid ended
The RPM's likely need to be rebuilt:
/bin/rm -rf /var/lib/rpm/__db.*
rpm --rebuilddb
/scripts/check_cpanel_rpms --fix
Then run
/scripts/upcp --force
The problem is that this file:
/var/cpanel/sysinfo.config
This line:
rpm_dist_ver=unknown
Needs to match the major version of the OS on the machine, for Centos 6.5:
rpm_dist_ver=6
Centos 5.x:
rpm_dist_ver=5