Question: After installing MySQL Community Server 5.59 (64bit) and MySQL Workbench 5.2.31a and setting it up I try accessing the db's configuration and receive the following error:

> 
> Configuration file 'C:\Program Files\MySQL\MySQL Server 5.0\my.ini' can not be found. New file will be created on apply of changes.
> 
> 
> 

I click OK. Then when trying to apply any change I get a second IO Error for not being able to write to the file.

It figures as my installation is at `C:\Program Files\MySQL\MySQL Server 5.5` and not at `C:\Program Files\MySQL\MySQL Server 5.0`. But why does Workbench search there?

Answer: 
I had the same issue with MySQL Server 5.7 and MySQL Workbench 6.3. The solution is quite simple. 

1. Open MySQL Workbench or switch to the **home page** with the connections
2. Click the small **tool icon** next to the label **MySQL Connections**
3. The **Manage Server Connections** dialog appears
4. Select the connection from the list of MySQL Connections
5. The **Connection** data for this connection appear to the right
6. Switch from the **Connection** tab to **System Profile**
7. Change the entry in the **Configuration File** field
8. Click the Close button and you are done

In my case all I had to do is to change the entry from:  

**%ProgramFiles%**\MySQL\MySQL Server **5.0**\my.ini  

to  

**%ProgramData%**\MySQL\MySQL Server **5.7**\my.ini
Your Server instance is registered wrong.

When you create new server instance for server administration in workbench, there is a selected option, e.g.:

> 
> Mysql Installation Type:
>  Window(MySQL5.0 x64 Installer Package)
> 
> 
> 

If you selected a wrong one with your current OS and Server installation, it would result an incorrect base path mapping.

To solve your issue, you can change the base directory in Server Administration-> Logging the instance -> Configuration Menu -> Configuration -> General:
1) Click the base directory checkbox
2) Input the path e.g. 

> 
> "C:/Program Files/MySQL/MySQL Server
>  5.1/"
> 
> 
> 

3) Click the data directory checkbox
4) Input the path e.g. 

> 
> "C:/Documents and Settings/All
>  Users/Application Data/MySQL/MySQL
>  Server 5.1/Data/"
> 
> 
>