Layout runs twice in page

I create a layout and paste the shortcode into the page, and it runs twice. That is, let’s say the layout has two posts, there are the first two posts and a space and then the next 2 posts! I’ve tried modifying every possible setting and no matter what I do, it’s as if the shortcode was pasted in twice. I can’t post a link because it’s running on my local server for testing, so hopefully I’ve described it well enough.

http://wordpress.org/extend/plugins/site-layout-customizer/