Oooooh, I figured out what it was. For some reason it wasn't saving my profile, but I set it to always keep my profile on and it's back and now I'm on the path back to redownloading everything. Sorry, fixed it =u=
Every time I close MO and re open it, all my mods are gone and uninstalled from the game and I need to redownload EVERYTHING over and over again. MO doesn't save profiles or anything and I REALLY need help with this because needing to reinstall every mod over and over again is agony. Someone please help?