I hope you are working on a fix since others are also running into same problem.
A little background that may help. The plugin was working when I first loaded it. I then loaded User Role Editor to restrict some access to the dashboard. It was working when I first loaded User Role Editor. As I was experimenting with settings I started to see problems. Items would show up on the Uploader list but not in my user_upload folder. Then I would see duplicates on my list but still no files in user-upload folder. Then it uploaded files but would not show up on the lists. I removed User Role Editor and that did not fix it. I then went into myPhp to remove all of user role editor tables that remained. That did not work. I deactivated and uninstalled a few other plugins. Still no luck. Based on my experience, it appears it is a user role setting. It would be interesting to hear if others with problems are using some type of role editor.