Content boxes not appearing after importing from backup

Hiya, this continues from my issues in the previous thread about these boxes but it's a separate issue to the uploading one.

I've rebuilt the site I was getting ready to launch on another domain and imported my content, menus etc to it. As soon as I did that it broke the Nelo theme and I've lost my three boxes on the homepage only.

On other pages there is a new horizontal divider in place that shouldn't be there either, but at least the boxes show.

Any idea what could be in my site import that could have caused this? In every other respect it was a blank, fresh WP install and there are no plugins running.