The problem is that you have not set the Strat's Mod Chooser to run as administrator and you probably didn't set the game folder to accept all permissions.
Uninstall game, reinstall by frowsing the game CD and right clicking Setup.exe and selecting Run as Administrator.. say no to GSA and Direct X.
Find the game filder Starfleet Command Orion Pirates and rigfht click on it, select Properties, uncheck Read Only and click Apply.. make sure that in the new pop up window All files and Folders is marked and click OK.. then click on Secruity tab.. then click Edit button and put a check makr into Full Access for every user / system / listing availble and click OK.. this will remove the game from Virtualization (as well as launching game as Administrator).
You can then alternatively install my OP Enhancement Package which includes a ton of scripts as well as OP + v4.0 and Mod Chooser.. you install this by running the file as administrator.. if you want to do the simple install, make sure to patch the game, run Mod Chooser, then run OP + v4.0, launch Mod Chooser to recognize it, then install Chris Jones Mod, then launch Mod Chooser again..
but make sure that each install is done as Administrator and every EXE you launch for SFC OP or Mod Chooser is run as administrator..
Also Chris Jones Mod includes Scripts as well.. I recommend backing up your scripts folder before installing.
and when you launch the game, create your own shortcut that points to StarfleetOP.exe.. the one the game installs points to SfcOP.exe and that game file has been bugged since launch and never updated..