I believe i have found a fix for this problem, as well as adding the 'sResourceDataDirsFinal=STRINGS\, TEXTURES\, MUSIC\, SOUND\, INTERFACE\, MESHES\, PROGRAMS\, MATERIALS\, LODSETTINGS\, VIS\, MISC\, SCRIPTS\, SHADERSFX\' Under [Archive] in Fallout4.ini and the 'bEnableFileSelection=1' Under [Launcher] in FalloutPrefs.ini, (basically all the stuff you're told to do to setup Fallout4 for modding and stuff), also add bInvalidateOlderFiles=1 sResourceDataDirsFinal= at the bottom of the [Archive] section in Fallout4.ini and leave a space between that and [Papyrus] (whatever the hell that means). This fixed the issue for me and it seems to work with both manual and NMM installed mods.