If you got it with Steam then the game is likely installed somwhere in the Steam folder in C:\Program Files\Steam. Windows UAC prevents the mod from modifying the game files. Ideally the game should not be installed in Program Files as the game relies on saving files into the Scenario folder. A solution may be to make a copy of the game folder and place this elsewhere on the c-drive. And run the subcommand executable from there. But iirc you also need to tweak a registry setting so the game knows where it's files are stored. I'm sure it is talked about in some thread in here over the years.
Also, the SCU program hacks the Subcommand executable to get different playable units, it's changing specific bytes inside. The Steam version of the file is different, and so SCU cannot work on this.
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