New Blog Template causes some theme options to be unavailable to new sites

I posted this in the Pro Sites category but it looks to be a New Blog Template issue, so I thought I'd try here.

In my network I have set up a template to automatically add the "Divi" theme to any newly created site. This works great EXCEPT that some of the theme functionality is lost in those new sites.

Here's a video screen capture that shows the problem I am facing: http://screencast.com/t/T4EMRaZh

Any ideas? Those features are pretty important to have working for all sites in my network.

FYI - I did try disabling all plugins, but with no success.

Thanks