Ahh, what Operation System do you have ?
I ask because I suspect that that's not the file the game actually uses, but a edited copy of it that's in your profile files, as the Operation System(s, Windows XP, Vista 7 and 8.1) protects the C:\Program Files (x86)\ sub-folder by mirroring the content and selectively using whatever they want.
To get over that and actually install mods, you have to install to a different folder than the C drives Program Files folders.
On Windows 8.1, the only folder on the C drive you can install games you wish to modify or even patch with official patches made before 2007 is the C:\Users\<username>\ sub-folders, where the <username> is the identity you log into the computer.