What I've tried:
1. Uploading images using customizer on several themes including Twenty Twelve.
2. Deactivated all plugins
3. Renamed "plugins" folder to "pluginsold" then logged in to backend and renamed back to plugins.
4. Used both latest Firefox & IE.
1. File gets uploaded to wp-content/uploads/2013/09.
2. an empty (0px x 0px) file is added to "your logo" in customizer.
3. For a few times an image placeholder showed where the logo would be. Don't know why that stopped.
4. no error messages.