Using Vortex, I think I have it figured out, partially. Vortex, when it stages FNIS in the Staging Folder unpacks a mod into a folder for that mod and redirects and builds to the Skyrim folders as needed, however because of this Vortex will often direct itself to the unpacked FNIS in it's staging folder, not the FNIS Generate for Users in the Skyrim Folders. This wouldn't be a problem (because of the redirects patch) but the Creatures addon is not built into the base FNIS folder in the Staging Folder, but is in the Skyrim Folders, so the FNIS Vortex generally uses by default doesn't find the Creature pack (Or often any other mods). Best workaround I can think of for now, is go into Vortex's settings, turn off the auto-run of FNIS option, then add the FNIS Generate for Users exe to the Dashboard for Skyrim SE in Vortex and just manually run it after deploying. For anybody else who checks this thread if they get that error in the future.
