The custom header is being shown in some places where it shouldn't be. It will appear in the media upload lightbox and in the upgrade plugin content area when a plugin is attempting to be reactivated after an upgrade.
For the media upload lightbox, you can do a check for
('media-upload.php' == basename($_SERVER['PHP_SELF']))
A workaround for the lightbox until you get this check added to the plugin is adding the following to your functions.php of your theme:
// There's a bug in the Custom Admin Branding plugin
if ('media-upload.php' == basename($_SERVER['PHP_SELF'])) {
remove_action('admin_head', 'custom_header', 11);
}
I'm not sure where the hook is for the plugin reactivation. You're on your own there. ;) But the output looks something like this
Files downloaded
Attempting reactivation of plugin
[header shows up here]
Plugin reactivated successfully.