Hmm. This is one of those rare intractable problems that happens to some people and never to others. It happened to me once and somehow cleared itself. Could you try:
– In Appearance > Customize, select “remove” on the logo and the favicon (if “remove” is visible);
– Exit Appearance > Customize;
– In media library, delete all copies of the logo and the favicon (making sure that you keep a copy on your own computer);
– Re-upload both.
No guarantees that it will work, though ??