Vendor is correct, if you are using Commander with GWX3 you also need to install the config files for the two of them to work together properly.
Also, it's unclear whether or not you installed a separate instance of JSGME on your computer... it's included with GWX3 so the most you should need to do is update to the latest version.
GWX3 should've created a desktop shortcut to the instance of JSGME that it installed in the game folder - when you open that, you should see all the optional GWX mods that it also put in the MODS folder it created for you.
Edit: and HBB is also correct about Starforce, if your copy of the game includes Starforce it will not want to play nice with Win7. Also UAC may interfere with attempts to mod games installed into the Programs folder so it's best to put your game installation elsewhere on your hard drive.
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