Windows Vista redirects writes to the Program Files folder to a folder in your users folder. It's an attempt to maintain compatibility with apps that expect to be able to write to these directories when the user running them does not have permissions to do so.
If you were saving that ini file with the 64bit version of notepad it would tell you that you didn't have permissions to save the file because 64bit apps are not subject to this redirection and will get to see the error. Basically the feature is confusing and not very helpful, but I guess they thought they would break too many windows 95 apps without it.
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