A temporary new installation of steam with skyrim thrown in seems to fix the problem. Using and old mod organiser version (1.01?) showed an oblivion install in a directory full of asian characters, likely a remnant from when steam once played up and reinstalled itself in E:x86 without any prompt from me. The skyrim install had the correct path, perhaps some data related was wrong and when MO followed that, it couldn't find skyrim, but would load the game listed in its own .ini file? Not smart enough to have a clue here.To anyone else having this problem, rename your steam folder so that shortcuts and registry keys won't work and reinstall steam somewhere else for skyrim's use. Consider deleting (or renaming) wherever windows keeps its game shortcuts, especially if youre seeing corrupted links like in oblivion above.