Some of those third-party mods might be considered as a vulnerability by the Windows and it wouldn’t let it pass through can cause this Fallout 4 mods not working issue. Since Nexus mods are open source, anyone can create a mod with the tool and post it on the store. Windows securities are getting much tighter these days due to plenty of vulnerabilities growing every day.
Read: Best Sites to Download Cracked PC Games For Windows 7/8/8.1/10 Method 2: Allow Through Firewall & Bypass Windows Security If you are still facing the issue, then simply go through the other methods below. Now try opening the game with your mods on and hopefully you don’t get any mods not working error anymore on Fallout 4.