I am trying to solve a somewhat similar problem that appears to somehow be related to file permissions. For me, I get the "file in use" dialog, but I can cancel it and the game loads and is playable in every other respect as far as I can tell.
I have found that MO also seems to alter file permissions for four files in the current profile including plugins.txt after starting the game. These files are shown in my second image at the Imgur album below--they are the files with the padlock superimposed on the icon. I can manually take ownership of these files as administrator after closing the game and MO, which removes the padlock, yet it does not eliminate the error on the next start.
I have tried manually taking ownership with my administrator-level account, ensuring that all users have full control, adding "Everyone" as a user with full control, replacing the profile with a new copy, and ensuring that all executables run as administrator. None of these steps have helped.
The behavior began after installing MO 1.1.1 and proximate to a CTD related to a missing master for one mod that I later corrected (this might have nothing to do with anything, but it is the context for when I noticed the error).
The images are at https://imgur.com/a/mlkav