The attachment_fields_to_edit method in the acf_everything_fields class doesn’t add custom fields if $screen is not empty.
if( !empty($screen) )
{
return $form_fields;
}
After uploading a file the attachment_fields_to_edit method is called but WordPress returns a WP_screen object for get_current_screen(). The screen object has an id of ‘async-upload’. I think ACF should probably continue (i.e. add the custom fields that have been configured) for this screen