There are a number of questions that need answered in order to help you.
1) What programming language and method(s) are you using to read/write to the ini file(s)?
2) Where are you placing the ini file(s)? In later versions of windows you should be placing these files in a folder that is completely user accessible, such as AppData (%APPDATA% variable contains this path for the current user), and probably not in the windows folder itself.