I have that file in both places as well. I had some issues a while back with FS9 CTD'ing shortly after launching the game. I tried all the usual suspects (FS9.cfg,ect) and had no luck. Then I copied the scenery.cfg from the main FS9 folder and over-wrote the one in Application Files and all was good. Not sure why there's 2 of them but I'm not complaining.
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