I solved this by using this code
function exclude_thumbnail_from_gallery($null, $attr)
{
if (!$thumbnail_ID = get_post_thumbnail_id())
return $null; // no point carrying on if no thumbnail ID
// temporarily remove the filter, otherwise endless loop!
remove_filter('post_gallery', 'exclude_thumbnail_from_gallery');
// pop in our excluded thumbnail
if (!isset($attr['exclude']) || empty($attr['exclude']))
$attr['exclude'] = array($thumbnail_ID);
elseif (is_array($attr['exclude']))
$attr['exclude'][] = $thumbnail_ID;
// now manually invoke the shortcode handler
$gallery = gallery_shortcode($attr);
// add the filter back
add_filter('post_gallery', 'exclude_thumbnail_from_gallery', 10, 2);
// return output to the calling instance of gallery_shortcode()
return $gallery;
}
add_filter('post_gallery', 'exclude_thumbnail_from_gallery', 10, 2);
Then uninstalling the Lightbox for Galleries plugin and then installing the jQuery Lightbox For Native Galleries.
Thank you all for your suggestions and help! 🙂