This is still an issue for us, but I realised why others might not be seeing the issue.
If we click on the edit icon on the course page when in editing mode it works fine. File uploads and shows up normally.
However, if you click on the folder link, and view the file list and then click the 'edit' button on the bottom right - we get the bugs described above.
Clicking on the Edit Settings in the Settings block also works normally.
If you try this you should notice that the interface is different - only a save changes button rather than 'save and return to course' or 'save and display'.
Can some other people please test this and verify?