In response to post #16216980. Had the same problem - it's because versions 50+ reset the Mod folders and install info locations. Go to the Skyrim tab under the Settings (the 'gear wheel') button and steer the folder locations to where you kept your Skyrim mod files on your computer. If you can't find them, I found if I uninstalled 50, and re-installed an older version then it gave me the right paths (which you can copy/refer to when you upgrade to the latest version again).