I had a problem along these lines for a couple of days just after I downloaded LOOT and the Skyrim editor. Everything was running ok until LOOT told me that Unofficial updates were dirty and needed TESVedit (or something like that). I watched a video on how to use the editor and cleaned the files. I used LOOT to set the load order. When I started the game from NMM with SKSE Skyrim started ok but the Sky UI didn't work. I'll cut this short, the load order got screwed up. Steam needs to start BEFORE SKSE I discovered. That was my temporary fix. If anyone knows how to set the load order so I don't have to manually start steam please post a reply.
