I do not know anything about Skyrim and modding with this, I have to admit. But your problem somehow sounded familiar: I am forced to work with an application every day that was designed for Unix once and had been ported to Windows-World. The scheme is the same:
- Open a file with application A
- Do something with the file
- close the file, but do not terminate the application
- Try deleting the file via Windows or something with application B while application A is still active - you fail!
Therefore, please don't hit me if I ask you: Is Skyrim itself really not active?
Second: Where did you install the application?
Third. Do you have access rights to the names file (You should if you did not install the stuff in a %\programs-folder)? Sometimes a file is marked as restricted for no reason.