@ perky416:
GWX overwrites and adds to the files in your existing SH3 game folder, rather than creating a second different game installation on your hard drive - so the same SH3.exe file that once opened the stock game now opens the GWX version instead. The stock game in that game folder has been overwritten by GWX. If you have a shortcut that already pointed to that file, plus a new one that GWX created when you installed it, they will both point to the same thing.
SH3 Commander will launch whatever SH3.exe file you point it to in its Options window, but I think the default is for the existing default game folder location, so if that's your only SH3 installation it should now also point to the GWX version that you installed on top of it.
Edit: did you also download and install the config files for SH3 Commander + GWX3? If not, you need to do that as well. They come in a handy little self installer so it's a relatively short and painless operation.