Alright, so there are multiple ways to proceed with this. 1: Make sure you aren't modifying the installation folder's SkyrimPrefs.ini but rather the one located in "My Documents" or just "Documents". 1a: Make sure you HAVE a My Documents folder, because if you don't then Skyrim will fail to launch any mods or none at all. 2: If the problem persists, then check your SkyrimPrefs.ini for any repeat [Launcher] segments, as this will cancel each other out and most likely won't launch any mods. 3: If the problem persists even more, quite persistent, then go to steam and right click Skyrim, then click on "Verify Files Integrity" or something like that. What that will do, is verify if your files are corrupted or not, and if they are then it will redownload the missing ones or the corrupted ones.