Updates: Also make sure that you have updates the Nexus Mod Manager to the latest version because the older versions were reported to cause issues with some Plugin files, therefore, causing issues with the Mods.

However, if you want to conserve space in a specific Hard Drive by installing the game on one and the Mods on another the Nexus Mod Manager does allow you to do this but in order to achieve this, you have to enable Multi HD Install during the installation process of the NMM.

Multi HD Install: Nexus Mod Manager works best if the Virtual Install is on the same Hard Drive as the game.

This can prevent the Nexus Mod Manager from loading the Mods because internet service might be essential for certain Mods.

Firewall: It is also possible that the Windows Firewall may be blocking certain elements of the game or the Nexus Mod Manager from making contact with the server.

If these files were not configured when Nexus Mod Manager was installed the Mods will not work with the game.

ini files inside the data folder of the game have to be properly configured to work with the Nexus Mod Manager and the game.

Fallout 4 textures take forever to load