This issue drove me crazy for a while after upgrading a site from 3.x to 4.6.2.  The solution, login as admin and go to the File Manager, there is a new section at the bottom where you have to assign the access rights to the directory in question.  It is better if you create a subdirectory just for documents.  You will see that the interface is similar to when you assign access rights to the module itself.

This should be documented a little better somehow to avoid the frustration of not seeing the files in the documents module.

Carlos