Try these tips.
First, turn off AV untill you are finished fully installing any and all applications, patches, utilites for the SFC game title. You need to install to the Program Files folder (32 bit) or the Program Files (x86) (64 bit).. you must launch the installer manually (not auto run) and install as administrator (right click setup.exe and run as administrator).. after installing the game, You need to find the install directory, right click the directory and select Properties, Uncheck the Read Only at the bottom of the General tab, click OK, say Yes for All files and Folders.. Next, you must patch to latest version by right clicking the patch and running as administrator, make sure the patch points to the proper install directory. Once installed, finde the Strfleet.exe, Starfleet2.exe, or StarfleetOP.exe and right click, go to properties, go to compatibility tab and set "Run as Administrator" check box. click OK.. right click the file again and select "Copy" and go to desktop and right click and select "Paste Shortcut". You will use this file to launch game (the other launcher files in Start Menu are bugged and can be deleted and removed from the Games folder).
For optimal performance you must set permissions to the current user, even if you are the administrator.
To do this, fine the Starfleet Command, Starfleet Command 2 (EAW depending on how you installed), or Starfleet Command Orion Pirates folder .. right click the folder, select Properties, select Security Tab. Click Edit button. Click Add Button. Type in your Windows Lon On name (the same name as your Pesonal folder .. the one where My Documents and My Download and My Videos is located). Click OK, then for each user listed, check Full Control and click Apply.. make sure to do this for each user listed. Once done, click OK and exit on out.
You can now install any mod packs etc for the SFC game series (if an EXE file, make sure to Run as Administrator AND point to the proper install directory).. when done, you can re-enable your Anti-Virus software.. run a scan of the game install directory to ensure everything is A-OK.. then get your game on.
Double check the patch.. Download it with the AV turned off.. sometimes the patch will corrupt when downloading with the AV enabled. You can scan the patch file after download is complete to ensure the safety of the file. when Patching the game, make sure the AV is turned off.. after patching is complete, you can scan your entire system if you like to ensure it is clean.