There are two Skyrimprefs.ini files !!!
....:\Games\Steam\steamapps\common\Skyrim\Skyrim<<<<
.....:\Users\"your user name"\Documents\My Games\Skyrim <<<<<<<<
For MO users, the SkyrimPrefs.ini file is in the ModOrganizer\profiles\profilename folder
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Try to uninstall Skyrim that way:
First do a standard uninstall. (Control Panel\All Control Panel Items\Programs and Features-> Uninstall The Elder Scrolls V: Skyrim)
Next, delete your skyrim folder under C:\Program Files (x86)\Steam\SteamApps\common\
Then delete your Skyrim directory under Documents/ My Games after backing up your save files if you wish.
Then under C:\Users\[Your Username]\AppData\Local\ - Delete the Skyrim folder that is in it.
(You should enable to see the hidden files under windows to delete that folder.) HOW: (View - Options - Folder Options - View - Advanced Settings: Show hidden files, folders and drives)
Use Ccleaner after all this (http://www.filehippo.com/download_ccleaner), and install your game again, from scratch. !!!!
You don't need to uninstall Steam.