New Blog Template not copying all settings to new subsites

I have a template site set up using the Pro Flexmarket theme from from Marketpressthemes.com. I’ve created page layouts and set them as the layouts for the home and store pages (as per theme developer instructions). I set this subsite to be the template in New Blog Templates. New sites are getting the theme applied (plus categories and pages set up in the template site) but the settings in the page layout aren’t being copied over to the new sites. Any idea why it isn’t copying that too?

The Flexmarket parent theme and Pro child theme are both network activated. The page builder part of the theme is controlled by Aqua Page Builder by http://aquagraphite.com/

(I just discussed this with @PC in live chat and he asked me to open a support ticket)