Thank for posting the my.ini

PROBLEM: You have the basedir and datadir under the [client] section

basedir and datadir are server-only options, not client program options.

SOLUTION : Remove them from under the [client] section and you are good to go !!!

When done, this

[client]
port= new_port

##The MySQL server
Path to installation directory. All paths are usually resolved relative to this.
basedir="C:/MySQL/"
#Path to the database root
datadir="C:/MySQL/"
#Set the default character set.
default-character-set=latin1

should now be this:

[client]
port= new_port

Give it a Try !!!

The options file in MySQL is a human-readable text file, typically called my.cnf on Unix and my.ini on Windows. This single file contains configuration entries for all things MySQL, including the server, and the client library, and the various other official client utilities.

The screen you're referring to is a glorified configuration file editor for that file.

Within the file there are "groups" with headers in brackets, that determine which portions of the file are read by the different components of MySQL -- the command line client hast its [mysql] section, the various client utilities (like mysqlcheck) will also read what's in [client], and the server itself is configured under [mysqld]. Some of the other utilities may also have their own optional sections, for utility-specific features and options that would not be valid for all client utilities, like [mysqldump].

What they're doing here is letting you edit different sections of a single file, without actually telling you what they're letting you do.

Take a look at your local options file, and this part of Workbench will perhaps be a little more intuitive.