You cannot use the C:\Program Files (x86) folder and then mod the game when dealing with older DirectX v9.0c games like SH3. Windows will fight you all the way, and will win. You need to move the game (and possibly Steam) to a different "Steam Library" folder. If you have multiple hard drives in the computer, that is a bit easier. If you have a laptop with only one hard drive, it is a bit more difficult. Refer to
Moving a Steam Installation and Games for more information on how to deal with this in Steam. If SH3 is the only Steam game, it is much easier. If you have a lot of Steam games, it is a pain in the #$$, but doable. Once you are out of the Program Files folders "protection" racket, you can use JSGME to apply mods, and they will take.
You will also have to check the SH3.exe file's "Properties" and make sure you
You will probably have to experiment with those settings. Some computers don't need but minimal help there, while others need them all. Almost all need the Compatibility settings, not many need the Program DPI at the top of the smaller properties page from the Change high DPI settings button.
Also, do not expect a wide screen mod to function with the Steam version of the game. Black Swan might come along and give you a PM to help out, but in the meantime, just be prepared for that inevitability...