Broken: 2.79. 5bd8ac9,
Worked: presumably never?
When rendering an animation while using compositing output nodes, you get doubled output because of the "write_still=True", when the ".base_path" of the output nodes and "bpy.data.scenes["Scene"].render.filepath" differ.
Exact steps for others to reproduce the error
In a new scene, go into the node editor, tick on "use nodes" and switch to the "compositing nodes" view.
Replace the "Composite" node with a "File Output" node.
Change its base path to "[...]\folder1"
Go into the "properties" area, into the render tab.
Under "output", change the folder to "[...]\folder2"
Render an animation, you will get an output in both folders.
I would suggest turning off the properties panel output path when "use nodes" is True and output nodes are present?