Hmm, I do know that a .ini file is basically just a renamed .txt with a specific set of rules on how a program writes to it. I've had experience with writing .ini's using Game Maker. All they really do is hold data externally of an executable.
Now, considering that it is named configuration settings, that is probably data on how your desktop appears, but I'm not too sure of that. I always thought that a file like that would just remain hidden. Does it appear like it is "phased out", like what Mario looks like with the invisible cap on in SM64?