Ordenador somehow fucked up my game

[unpronounceable]

I ran ordenador because I was led on by tales of smoother frame rates.

Unfortunately, when I ran it on my mods folder in Mod Organizer, it fucked up the game somehow, making it impossible to both start new games and to load saves.
When I launch the game outside of MO, the game can start fine.

The weird part is, I backed up my mods folder before I ran Ordenador. 

I replaced the mods folder with my backup and the game STILL CRASHES.

Is it possible that ordenador modified files outside of the folder I specified?