I've used the upcp script several times in the past to force updates when needed, however for the last week I've attempted many times and it seems to die right after it says MySQL-4.0.25 is up to date.
Code:
MySQL Setup Script Version 6.0
Fetching version information from http://updates.cpanel.net/mysqlinstall/version (EDGE)....Done
This is the MySQL 4.0.25 installer release number 0 for platform
MySQL-4.0.25 is up to date