I had a problem similar to this. Loot, xEdit, Wrye Bash could all see my mods, but for some reason, FNIS and SkyrimSE itself could not. I ended up formatting my drive and reinstalling Windows and everything. That fixed my problem. It may have been some screwy registry or appdata issue that I doubt I would have been able to figure out in a timely fashion... so a complete reinstall of Windows was my solution. Probably not the best solution though...