phpMyAdmin and mysql not showing the same database
The database server that you are accessing using phpmyadmin and the mysql monitor (command line client) are different. If you look at the versions, phpmyadmin is accessing a 5.5.1-m2-community version, while you are accessing 5.6.17-community on the command line.

Either you are accessing a remote server or you have two separate installations of mysql on the server. If the later, use netstat -aon | more or the Task Manager to locate the mysql processes running on your machine (and on which port they are listening).