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NTFS stands for NT File System. Which is what most windows servers configured for production environments use as their file system.
With windows, you need to set the file as read only through the operating system (as opposed to setting the permissions of the web server accounts) in order to get the message to go away.
This can be done by opening windows explorer (from the server), finding mainfile.php, right clicking, choosing properties, and setting the attributes to READ ONLY.
Notice that this does not have anything to do with the web server (IIS) or the accounts that the web server is running, but is done at an operating system (windows) level.
It is very confusing because you can also protect the file by IIS Account permissions which is what you were talking about re: single reading" for the common user and "total control" for the administrator and server...
If you set all of the accounts above (common user, administrator, and server) to 'read'... it does the same thing as far as restricting access (well almost), but the message in your administration section will remain. The reason is that the script checks to see if the file is writeable by the operating system.
Hope that helps