This plugin allows you to customize WordPress by adding support to upload custom login logo, favicon & Apple touch icon and by hiding non essentia
It seems that plugin use old WP uploader that not working completely in WP 3.9.
I can upload an image to Media library but when I press Insert button nothing happens. So I just copy URL of uploaded file and paste it to text field.
But you must use attachment ID's instead of URLs because I can upload 1500✕1500 image and insert it's URL that will be loaded longer than 512✕512 image that you can convert via plugin with attachment ID.