Why can't I see a complete list of MySQL processes when using phpMyAdmin?
This appears to be apart of the limitations of how the database users are configured, as while the cPanel user (which has its own database user associated with it) can create individual database users; the users are mapped to the cPanel users, but not owned by the database user which accesses PHPMyAdmin.
For example, the cPanel account has a user named "username" which accesses PHPMyAdmin and PHPMyAdmin can view the processes started by "username". However, it cannot view the processes started by "username_user" as the user is independent of the "username" user and "username" doesn't have access to its mapped user's process information directly with how PHPMyAdmin is configured to be accessed.
When needing to view the running MySQL processes, you can still view all of the processes via the root or any other super privileged user login for WHM. When trying to narrow down the user processes, you could also use the "mysqladmin proc" command and grep for the user (although for users with usernames longer than eight characters, you will need to limit the grep to the first eight characters).