I don't access to the same set of databases when connecting to MySQL service (or "Mysqld.exe") through command line, or through "MySQL Notifier".

The set of databaese changes when I execute SHOW DataBases; in command line, and in the windows file explorer: C:\ProgramData\MySQL\MySQL Server 5.6\data

Are mysqld and MySQL Notifier running two different instances of MySQL server 5.6?