Whenever I use Mod Organizer to start a program (SKSE, LOOT, Tes5Edit etc) the FNIS patcher comes up instead of launching the game. When this happened for the first time I just thought maybe MO is stuffing up and tried directly launching it through skse in the Skyrim directory. Well, it launched but the game was completely vanilla vanilla and no one had heads. (I.E my mods didn't work).