Check_MK Windows Agent

The ini files needs to be inside the /config folder. This folder is for 1.6 C:\ProgramData\checkmk\agent\config

Naming - from the plugin comments

    ' Use either an instance specific config file named mysql_<instance-id>.ini
    ' or the default mysql.ini file.

The file is then used as a –defaults-extra-file for the mysql call.
That means the content of the config file must be the same format as inside a –defaults-extra-file.

This message means your are inside the WATO and not in your normal status view. Inside WATO checks with counters cannot be done as you need two or more intervals to get an result.
Activate your changes and look at the service status view of your host.