URE does not prevent access to the media library items for the test user with added custom filter. It works with the folders also when you open Media Library directly via menu “Media Library”. I see that “WP Media Folder” plugin does not open folders when you try to access them from the post editor page.
URE should not prevent that. Some conflict between plugins takes place here.
You have at your site an older version 2.4.1 of WP Media Folder plugin.
My test with a much later version 4.2.7 of WP Media Folder plugin from Joomunited shows that this conflict was gone. Restricted user has access to the images in any folder as from Media Library directly as via post editor page.
If that’s suitable for you I would recommend to update your version of WP Media Folder plugin to the latest one.