[Pisces]

First off, I presume you downloaded the SH3 Commander files from a reputable source? Like here, the download section?

SH3 Commander changes files and folders in it's own and the SH3 game root-folder. JSGME change files in the game's root folder as well. For that reason, it is best to NOT install Commander and the game in the default location inside c:\Program Files-something. Direct it to something like c:\Games\SilenthunterIII or similar for SH3 Commander. That avoids UAC popups and quarantined file-changes that break your intended modifications. (to start JSGME it comes with a UAC popup anyway on my system because I am non-administrator user)

You may also need to put an exception in your virusscanner software to prevent Commander getting blocked by it. And still Windows might warn you if it detects the program doing 'dangerous' things (Windows Defender Smartscreen window). But you can by pass it to start it anyway, if it shows a proceed button or link.

I have no personal experience with a Steam install, so you might need to search the forum for instructions on that. I know there are.