MSE/Defender may need to be disabled in two different places, which can complicate things, although I don't know if it was the same back on Windows 7. Problems caused by Windows Defender (strange behavior when using Opus) has details (but is written for Windows 10).
You can override the flags when opening layouts, but you'd have to do that specifically in the command that was using the layouts, and it wouldn't change what you see in Preferences.
Type /dopusdata\Layouts into the path field and you'll see all the saved layouts.
The timestamp on the edited layout should change if you change a flag on it and click OK or Apply in Preferences.