Anonymity

I was having similar issues. Loot, skse, and all other executables would crash when launched through MO. I followed GSDFan's advice and I happened to fix it by disabling a mod called "Infinite Blade Armor". I looked into why it was causing me problems and it seemed to have something to do with a stray BSA file outside the data folder. I deleted the rogue BSA and things started working again. My guess is that either the BSA was corrupt or there was a problem with the way the files were organized. Perhaps there's a mod like that with your setup?