I disabled all my active mods before doing a clean install of Skyrim, I figured i might as well start fresh. I only noticed the problem when i got to the 'create the skyrim revisited profile' section, specifically the part where you use the MO to install the SKSE data folders, when i ran it i got the boxes. I then ran the vanilla skyrim file and it was the same, so i'm pretty stumped? I could just start again from scratch, it's not like i'm far into the install?