I can confirm, my situation was I had my mod organiser at the root of my HDD for the downloads. Because I dont want to use space on my SSD. So i created a mod folder inside my skyrim (which is like 9 folders deep). GenerateFNIS_for_Users.exe also had a similar problem where if your mod organiser mod directory is too deep into a directory it will not function. I just copied my mods to the base directory of the mod organiser (Which i cut to my SSD from my HDD). Changed the preferences and taadaah. Ran relinker and it worked. Thanks for the help guys!