In addition, many files can be moved around without adverse effects, within limits as it 'groups' plugins. Sometimes it needs manual assistance, which is why it has 'metadata' to permit you to configure it for those situations it doesn't know how to handle correctly. While I use and recommend LOOT, it is not 100% perfect.
* Do you have a 32-bit or 64-bit version of Windows 8.1? * Do you have NVSE or any of it's plugins installed? Otherwise you will spend a lot of time and effort trying other solutions, and still have to move the game files in the end anyway. This should be the first solution you try. That article has a link to the official Steam Procedure (a good indication that they now recognize the need to correct this). As painful as it may sound, read the wiki article Installing Games on Windows Vista+ and move at least FNV.
* Did you install Steam under the default location of the 'C:\Program Files' tree? This causes many 'strange' problems not otherwise explainable. But additional information we ask for in the 'How to ask for help' article (and still need) is: