If the Nexus Mode Manager does not have administrative privileges, it might prevent mods from working.
ini files in the data folder may cause this issue. Several reasons might be behind this issue some of which are listed below. This problem is reported by many gamers worldwide. Fallout 4 mods not working What prevents Mods from working in Fallout 4? There is nothing to worry about because the “ Fallout 4 Mods not Working” problem on Xbox and PC has a solution and can be resolved in very little time. Many users around the world have reported this problem. Sometimes when you launch the game Fallout 4 and start playing, it’s mods suddenly stop working and the game crashes or sometimes any other errors also occur due to it such as black screens and Script extender not working.