SOLVED: You have to make Vortex use the Skyrim\Data\tools\GenerateFNIS_for_Users version file NOT the one from the vortex mods folder. The one in your Vortex dir is inactive and will not work. Alternatively (what I did), you can run the GenerateFNISforUsers.exe inside of Skyrim\Data\tools\GenerateFNIS_for_Users when you download FNIS mods.
I have moved my mods directory, and FNIS won't get my animations from OSA FNIS Error: I believe this to be a vortex error, b/c the file redirection option is not working. When I deselect it FNIS complies fine.