That's strange. I have had 0 problems with ut2004. And following the directions from the
latest patch, i have even gotten my name on the hellbender license plate, and i'm getting great fps lately. If you still have that problem you should make a launch ut2004 script that copies over the User.ini every time so you won't have to worry about that problem anymore.
BTW, about mv, mv will only copy over files with same name, not directories, it'll just dump stuff from the directory witht the same name to the other.