Are you trying to use it in a template, rather than in the content area?
I ran in to the same problem using Flex Slider in a template like so:
echo do_shortcode("[metaslider id=999]");
Simple Lightbox isn’t “triggered” by this – no JS winds up on the page, so it won’t work. You need to instantiate simple light box through the ‘slb_activate’ function, like so (in your template):
$content = do_shortcode("[metaslider id=999]");
if ( function_exists('slb_activate') )
$content = slb_activate($content);
echo $content;
Good luck