Is the Documents folder the one which the top file display opens with initially?
If so, please try going up to the Libraries folder (as you are in your screenshot), then saving that as the default lister (Settings > Set as Default Lister). Then close any open windows and open a new one. It should open in the Libraries folder, as when you saved it.
After doing that, do you still have two Documents libraries in the tree?
If you don’t, and it looks correct now, please set up the default lister to start in the Documents library again, similar to above, and then see if the problem comes back. My hope is that it won’t come back after doing that, but it depends on the exact cause of the extra tree item.