I've moved your post to the Skyrim SE specific version of FNIS as that is what you are running.
Question: how are you using MO for SSE?
There is a plugin on the SSE nexus which you put in the modorganizer/plugins folder. this let mod organizer recognize SSE. It does not support nmm links, so you have to dl mods manually. i found out that you can dl the mods into mod organizer's downloads folder which will let you install them easier through the downloads tab.
The version/update function does not work, the archive handler does not work, wrye bash compatability is just bare minimum (wrye can read your files, but cant enable/disable, bashed patches appear in the data folder)
MO crashes freqently, often during installs (most of them install properly, just MO freezing)