I have a WP site that uses a non-standard location for file uploads. Instead of wp-content/uploads I have it set to /files in the settings. When I upload the logo via your plugin admin, it goes to the right place, but does not insert the image from there. When I inspected the database, i found that it hard coded the link to the image as being in wp-content/uploads. Example: http://example.com/wp-content/uploads/image.jpg vs. http://example.com/files/image.jpg