Thank you for the prompt response and solution tips.
I am using the latest WP 3.6.1
I've tried to de-activate and re-activate and this seems to have solved the issue and the smart layers now appear normally.
But when I try to customize it with my own settings that's where it disappears again!
I've used the dev build, and it works even with changing settings and customization.
By the way, I wanted to know whether your scripts gets called in the header or footer? as I wanted to move my scripts to the footer so they don't slow down the site loading as recommended by Google page speed service. And I wonder if that's an option that you can provide within the plugin settings?